********> update.10 Author: Feng Pan Date: October 8, 2018 Programs: sander Description: 1) Add the contribution of potential energy from all the NFE restraints to the total potential energy 2) Make NFE modules compatible with REMD methods 3) Fix several bugs related with selection algorithm in ABMD 4) Modify related test files -------------------------------------------------------------------------------- AmberTools/src/sander/force.F90 | 18 +- AmberTools/src/sander/mdread1.F90 | 9 - AmberTools/src/sander/nfe-abmd-hooks.F90 | 215 +++-------- AmberTools/src/sander/nfe-bbmd-ctxt.F90 | 48 ++- AmberTools/src/sander/nfe-bbmd-hooks.F90 | 26 +- AmberTools/src/sander/nfe-pmd-hooks.F90 | 143 +++----- AmberTools/src/sander/nfe-sander-hooks.F90 | 74 ++-- AmberTools/src/sander/nfe-sander-proxy.F90 | 43 +++ AmberTools/src/sander/nfe-smd-hooks.F90 | 29 +- AmberTools/src/sander/nfe-stsm-hooks.F90 | 270 ++------------ AmberTools/src/sander/remd.F90 | 30 -- AmberTools/src/sander/runmd.F90 | 15 +- test/nfe/abmd_ANALYSIS/run-pmemd.sh | 2 +- test/nfe/abmd_ANALYSIS/run-sander.sh | 2 +- test/nfe/abmd_ANALYSIS/save.pmemd/mdout | 123 ++++--- test/nfe/abmd_ANALYSIS/save.sander/mdout | 151 +++++--- test/nfe/abmd_FLOODING/save.pmemd/mdout | 204 +++++++---- test/nfe/abmd_FLOODING/save.sander/mdout | 196 ++++++---- test/nfe/abmd_UMBRELLA/save.pmemd/mdout | 204 +++++++---- test/nfe/abmd_UMBRELLA/save.sander/mdout | 195 ++++++---- test/nfe/abremd/inpcrd.1 | 2 +- test/nfe/abremd/inpcrd.2 | 2 +- test/nfe/abremd/inpcrd.3 | 2 +- test/nfe/abremd/inpcrd.4 | 2 +- test/nfe/abremd/mdin.1 | 2 +- test/nfe/abremd/mdin.2 | 2 +- test/nfe/abremd/mdin.3 | 2 +- test/nfe/abremd/mdin.4 | 2 +- test/nfe/abremd/run-pmemd.sh | 65 ++++ test/nfe/abremd/run-sander.sh | 11 +- test/nfe/abremd/save.pmemd/abmd.1.txt | 53 +++ test/nfe/abremd/save.pmemd/abmd.2.txt | 28 ++ test/nfe/abremd/save.pmemd/abmd.3.txt | 20 + test/nfe/abremd/save.pmemd/abmd.4.txt | 13 + test/nfe/abremd/save.pmemd/mdout.1 | 445 +++++++++++++++++++++++ test/nfe/abremd/save.pmemd/mdout.2 | 445 +++++++++++++++++++++++ test/nfe/abremd/save.pmemd/mdout.3 | 445 +++++++++++++++++++++++ test/nfe/abremd/save.pmemd/mdout.4 | 445 +++++++++++++++++++++++ test/nfe/abremd/save.pmemd/rem.log | 56 +++ test/nfe/abremd/save.pmemd/umbrella.1.ncdump | 41 +++ test/nfe/abremd/save.pmemd/umbrella.2.ncdump | 41 +++ test/nfe/abremd/save.pmemd/umbrella.3.ncdump | 41 +++ test/nfe/abremd/save.pmemd/umbrella.4.ncdump | 41 +++ test/nfe/abremd/save/abmd.1.txt | 110 +++--- test/nfe/abremd/save/abmd.2.txt | 55 ++- test/nfe/abremd/save/abmd.3.txt | 37 +- test/nfe/abremd/save/abmd.4.txt | 20 +- test/nfe/abremd/save/mdout.1 | 336 ++++++++++------- test/nfe/abremd/save/mdout.2 | 330 ++++++++++------- test/nfe/abremd/save/mdout.3 | 336 ++++++++++------- test/nfe/abremd/save/mdout.4 | 334 ++++++++++------- test/nfe/abremd/save/rem.log | 82 ++--- test/nfe/abremd/save/umbrella.1.ncdump | 41 +++ test/nfe/abremd/save/umbrella.2.ncdump | 41 +++ test/nfe/abremd/save/umbrella.3.ncdump | 41 +++ test/nfe/abremd/save/umbrella.4.ncdump | 41 +++ test/nfe/bbmd/run-pmemd.sh | 13 +- test/nfe/bbmd/save.pmemd/mdout.1 | 264 ++++++++------ test/nfe/bbmd/save.pmemd/mdout.2 | 272 ++++++++------ test/nfe/bbmd/save.pmemd/mdout.3 | 278 ++++++++------ test/nfe/bbmd/save.pmemd/mdout.4 | 246 +++++++------ test/nfe/bbmd/save.sander/mdout.1 | 180 +++++---- test/nfe/bbmd/save.sander/mdout.2 | 203 +++++++---- test/nfe/bbmd/save.sander/mdout.3 | 203 +++++++---- test/nfe/bbmd/save.sander/mdout.4 | 157 +++++--- test/nfe/common.sh | 32 +- test/nfe/mwabmd/mdin.1 | 2 +- test/nfe/mwabmd/mdin.2 | 2 +- test/nfe/mwabmd/mdin.3 | 2 +- test/nfe/mwabmd/mdin.4 | 2 +- test/nfe/mwabmd/run-pmemd.sh | 12 +- test/nfe/mwabmd/run-sander.sh | 12 +- test/nfe/mwabmd/save.pmemd/abmd.1.txt | 78 ++-- test/nfe/mwabmd/save.pmemd/abmd.2.txt | 50 +-- test/nfe/mwabmd/save.pmemd/abmd.3.txt | 33 +- test/nfe/mwabmd/save.pmemd/abmd.4.txt | 20 +- test/nfe/mwabmd/save.pmemd/mdout.1 | 323 +++++++++------- test/nfe/mwabmd/save.pmemd/mdout.2 | 273 ++++++++------ test/nfe/mwabmd/save.pmemd/mdout.3 | 271 ++++++++------ test/nfe/mwabmd/save.pmemd/mdout.4 | 267 ++++++++------ test/nfe/mwabmd/save.pmemd/umbrella.1.ncdump | 41 +++ test/nfe/mwabmd/save.pmemd/umbrella.2.ncdump | 41 +++ test/nfe/mwabmd/save.pmemd/umbrella.3.ncdump | 41 +++ test/nfe/mwabmd/save.pmemd/umbrella.4.ncdump | 41 +++ test/nfe/mwabmd/save.pmemd/wt_umbrella.1.ncdump | 41 +++ test/nfe/mwabmd/save.pmemd/wt_umbrella.2.ncdump | 41 +++ test/nfe/mwabmd/save.pmemd/wt_umbrella.3.ncdump | 41 +++ test/nfe/mwabmd/save.pmemd/wt_umbrella.4.ncdump | 41 +++ test/nfe/mwabmd/save.sander/abmd.1.txt | 78 ++-- test/nfe/mwabmd/save.sander/abmd.2.txt | 50 +-- test/nfe/mwabmd/save.sander/abmd.3.txt | 33 +- test/nfe/mwabmd/save.sander/abmd.4.txt | 20 +- test/nfe/mwabmd/save.sander/mdout.1 | 339 +++++++++-------- test/nfe/mwabmd/save.sander/mdout.2 | 266 ++++++++------ test/nfe/mwabmd/save.sander/mdout.3 | 266 ++++++++------ test/nfe/mwabmd/save.sander/mdout.4 | 268 ++++++++------ test/nfe/mwabmd/save.sander/umbrella.1.ncdump | 41 +++ test/nfe/mwabmd/save.sander/umbrella.2.ncdump | 41 +++ test/nfe/mwabmd/save.sander/umbrella.3.ncdump | 41 +++ test/nfe/mwabmd/save.sander/umbrella.4.ncdump | 41 +++ test/nfe/mwabmd/save.sander/wt_umbrella.1.ncdump | 41 +++ test/nfe/mwabmd/save.sander/wt_umbrella.2.ncdump | 41 +++ test/nfe/mwabmd/save.sander/wt_umbrella.3.ncdump | 41 +++ test/nfe/mwabmd/save.sander/wt_umbrella.4.ncdump | 41 +++ test/nfe/pmd/run-pmemd.sh | 2 +- test/nfe/pmd/run-sander.sh | 2 +- test/nfe/pmd/save.pmemd/mdout | 166 +++++---- test/nfe/pmd/save.sander/mdout | 174 +++++---- test/nfe/pmd/save.sander/pmd.txt | 2 +- test/nfe/premd/inpcrd.1 | 2 +- test/nfe/premd/inpcrd.2 | 2 +- test/nfe/premd/inpcrd.3 | 2 +- test/nfe/premd/inpcrd.4 | 2 +- test/nfe/premd/mdin.1 | 2 +- test/nfe/premd/mdin.2 | 2 +- test/nfe/premd/mdin.3 | 2 +- test/nfe/premd/mdin.4 | 2 +- test/nfe/premd/run-pmemd.sh | 49 +++ test/nfe/premd/run-sander.sh | 4 +- test/nfe/premd/save/mdout.1 | 329 ++++++++++------- test/nfe/premd/save/mdout.1.pmemd | 429 ++++++++++++++++++++++ test/nfe/premd/save/mdout.2 | 320 +++++++++------- test/nfe/premd/save/mdout.2.pmemd | 429 ++++++++++++++++++++++ test/nfe/premd/save/mdout.3 | 324 ++++++++++------- test/nfe/premd/save/mdout.3.pmemd | 429 ++++++++++++++++++++++ test/nfe/premd/save/mdout.4 | 328 ++++++++++------- test/nfe/premd/save/mdout.4.pmemd | 429 ++++++++++++++++++++++ test/nfe/premd/save/pmd.1.txt | 112 +++--- test/nfe/premd/save/pmd.1.txt.pmemd | 56 +++ test/nfe/premd/save/pmd.2.txt | 112 +++--- test/nfe/premd/save/pmd.2.txt.pmemd | 56 +++ test/nfe/premd/save/pmd.3.txt | 112 +++--- test/nfe/premd/save/pmd.3.txt.pmemd | 56 +++ test/nfe/premd/save/pmd.4.txt | 112 +++--- test/nfe/premd/save/pmd.4.txt.pmemd | 56 +++ test/nfe/premd/save/rem.log | 82 ++--- test/nfe/run-pmemd-parallel.sh | 2 +- test/nfe/smd/run-pmemd.sh | 2 +- test/nfe/smd/save.pmemd/mdout | 204 +++++++---- test/nfe/smd/save.sander/mdout | 211 +++++++---- test/nfe/smd2/run-sander.sh | 2 +- test/nfe/smd2/save.pmemd/mdout | 149 +++++--- test/nfe/smd2/save.sander/mdout | 175 ++++++--- 143 files changed, 11236 insertions(+), 4873 deletions(-) diff --git AmberTools/src/sander/force.F90 AmberTools/src/sander/force.F90 index ea6d62f36f..f0ac20e02d 100644 --- AmberTools/src/sander/force.F90 +++ AmberTools/src/sander/force.F90 @@ -38,15 +38,7 @@ subroutine force(xx, ix, ih, ipairs, x, f, ener, vir, fs, rborn, reff, & #ifndef DISABLE_NFE use nfe_sander_hooks, only: nfe_on_force => on_force -# if !defined(LES) && defined(MPI) - use remd, only: rem, mdloop -# endif -# ifdef MPI - use nfe_sander_proxy, only: nfe_remember_initremd => remember_initremd, & - infe -# else use nfe_sander_proxy, only: infe -# endif /* MPI */ #endif /* DISABLE_NFE */ use file_io_dat #ifdef LES @@ -192,7 +184,7 @@ subroutine force(xx, ix, ih, ipairs, x, f, ener, vir, fs, rborn, reff, & logical, intent(out) :: do_list_update _REAL_ enmr(6), devdis(4), devang(4), devtor(4), devpln(4), devplpt(4), & - devgendis(4), entr, ecap + devgendis(4), entr, ecap, enfe _REAL_ x(*), f(*), vir(4) type(state_rec) ener @@ -312,6 +304,7 @@ subroutine force(xx, ix, ih, ipairs, x, f, ener, vir, fs, rborn, reff, & dvdl = 0.d0 dipole_temp = 0.d0 enmr(1:6) = 0.d0 + enfe = 0.d0 vir(1:4) = 0.d0 virvsene = 0.d0 f(1:3*natom+iscale) = 0.d0 @@ -356,10 +349,7 @@ subroutine force(xx, ix, ih, ipairs, x, f, ener, vir, fs, rborn, reff, & #ifndef DISABLE_NFE if (infe == 1) then -# ifdef MPI - call nfe_remember_initremd(rem .gt. 0 .and. mdloop .eq. 0) -# endif - call nfe_on_force(x, f) + call nfe_on_force(x, f, enfe) end if #endif @@ -1086,7 +1076,7 @@ subroutine force(xx, ix, ih, ipairs, x, f, ener, vir, fs, rborn, reff, & endif #endif pot%constraint = pot%constraint + eshf + epcshf + pot%noe + & - sum(enmr(1:6)) + ealign + ecsa + pot%emap + xray_e + sum(enmr(1:6)) + ealign + ecsa + pot%emap + xray_e + enfe #ifdef DSSP pot%constraint = pot%constraint + edssp #endif diff --git AmberTools/src/sander/mdread1.F90 AmberTools/src/sander/mdread1.F90 index c33347aec2..dff72e86fe 100644 --- AmberTools/src/sander/mdread1.F90 +++ AmberTools/src/sander/mdread1.F90 @@ -38,9 +38,6 @@ use emil_mod, only : emil_do_calc use mdin_emil_dat_mod, only : error_hdr -#if !defined(DISABLE_NFE) && defined(MPI) - use nfe_sander_hooks, only : nfe_on_mdread1 => on_mdread1 -#endif /* ! DISABLE_NFE && MPI */ #ifndef API use xray_interface_module, only: xray_active, xray_read_mdin #endif /* API */ @@ -1255,12 +1252,6 @@ if (hwtnm1 /= ' ') read(hwtnm1,'(A4)') ihwtnm(1) if (hwtnm2 /= ' ') read(hwtnm2,'(A4)') ihwtnm(2) -#if !defined(DISABLE_NFE) && defined(MPI) - if ( infe == 1 ) then - call nfe_on_mdread1() - end if -#endif - return #ifndef API diff --git AmberTools/src/sander/nfe-abmd-hooks.F90 AmberTools/src/sander/nfe-abmd-hooks.F90 index 839ba644d7..b1cc432ff7 100644 --- AmberTools/src/sander/nfe-abmd-hooks.F90 +++ AmberTools/src/sander/nfe-abmd-hooks.F90 @@ -12,9 +12,7 @@ use nfe_umbrella, only : umbrella_t, & use nfe_colvar_type, only : colvar_t -#ifdef MPI -use nfe_constants, only : ABMD_REMLOG_UNIT -#endif /* MPI */ +use random implicit none @@ -24,11 +22,12 @@ private ! T H E H O O K S !----------------------------------------------------------------------------- -! multisander.f +! old REMD subroutines, not used now -------- #ifdef MPI public :: on_delta public :: on_exchange #endif /* MPI */ +! ------------------------------------------- public :: on_multisander_exit !----------------------------------------------------------------------------- @@ -58,8 +57,6 @@ public :: on_mdwrit integer, private, parameter :: MONITOR_UNIT = ABMD_MONITOR_UNIT integer, private, parameter :: CV_UNIT = ABMD_CV_UNIT -character(*), private, parameter :: SECTION = 'nfe_abmd' - character(*), private, parameter :: & DEFAULT_MONITOR_FILE = 'nfe-abmd-monitor', & DEFAULT_UMBRELLA_FILE = 'nfe-abmd-umbrella', & @@ -112,9 +109,10 @@ integer, private, save :: nhills ! not zeroed on exchange integer, private, save :: selection_freq = 0 NFE_REAL, private, save :: selection_constant = 1.0 NFE_REAL, private, save :: selection_epsilon = 0.0 +type(rand_gen_state), save :: nfe_abmd_gen ! Well-tempered ABMD NFE_REAL, private, save :: pseudo = 0.0 -double precision, private, save :: wt_temperature = 0.0 +NFE_REAL, private, save :: wt_temperature = 0.0 ! Driven ABMD integer, private, save :: drivenw integer, private, save :: drivenu @@ -145,12 +143,9 @@ character(len = SL), private, save :: MDOUT_FILE ! Moradi end ! -! rem-specific +! rem-specific, for old subroutiens, not used now ! -character(*), private, parameter :: REMLOG_FILE = 'nfe-abmd.log' -integer, private, parameter :: REMLOG_UNIT = ABMD_REMLOG_UNIT - ! rem_* arrays live on sander masters; indexed by masterrank character(len = SL), private, allocatable, save :: rem_monitor_files(:) @@ -311,14 +306,10 @@ subroutine on_multisander_exit() end if #endif /* NFE_ENABLE_BBMD */ ! Moradi end - - if (multisander_rem().eq.1) & - call rem_cleanup() #endif /* MPI */ if (imode.eq.MODE_FLOODING.or.imode.eq.MODE_UMBRELLA) & call umbrella_fini(umbrella) - NFE_MASTER_ONLY_END imode = MODE_NONE @@ -332,11 +323,7 @@ end subroutine on_multisander_exit ! MPI is initialized and MDIN/PRMTOP/INPCRD are loaded ! -#ifdef MPI -subroutine on_sander_init(mdin_name, mdin_unit, amass, rem_idx) -#else subroutine on_sander_init(mdin_unit, amass) -#endif /* MPI */ use nfe_utils use nfe_colvar @@ -351,15 +338,9 @@ subroutine on_sander_init(mdin_unit, amass) NFE_REAL, intent(in) :: amass(*) -#ifdef MPI - integer, intent(in) :: rem_idx - character(SL), intent(in) :: mdin_name -#endif /* MPI */ - - logical :: umbrella_file_exists + logical :: umbrella_file_exists, do_transfer type(umbrella_t) :: umbrella_from_file - logical :: do_transfer integer :: n, error integer :: cv_extents(UMBRELLA_MAX_NEXTENTS) @@ -375,71 +356,20 @@ subroutine on_sander_init(mdin_unit, amass) #ifdef MPI # include "nfe-mpi.h" - integer, allocatable :: perm(:) - integer, save :: counter = 0 +# include "../include/md.h" #endif /* MPI */ + integer, save :: counter = 0 - mdstep = 0 ! used in on_force() below do_transfer = .false. + if(counter == 0) mdstep = 0 ! used in on_force() below + #ifdef MPI if (counter.gt.0) then nfe_assert(multisander_rem().ne.0) NFE_MASTER_ONLY_BEGIN if (imode.ne.MODE_NONE) then - - ! re-arrange rem_* arrays - - allocate(perm(mastersize), stat = error) - if (error.ne.0) & - NFE_OUT_OF_MEMORY - - call mpi_allgather(exchange_partner, 1, MPI_INTEGER, & - perm, 1, MPI_INTEGER, commmaster, error) - nfe_assert(error.eq.0) - - if (imode.ne.MODE_ANALYSIS) & - call umbrella_swap(umbrella, rem_umbrellas(masterrank)) - - do n = 0, mastersize - 1 - if (n.gt.perm(n + 1)) then - - call swap(rem_monitor_files(n), rem_monitor_files(perm(n + 1))) - call swap(rem_monitor_freqs(n), rem_monitor_freqs(perm(n + 1))) - - if (imode.eq.MODE_FLOODING) then - call swap(rem_snapshots_freqs(n), & - rem_snapshots_freqs(perm(n + 1))) - call swap(rem_snapshots_basenames(n), & - rem_snapshots_basenames(perm(n + 1))) - call swap(rem_umbrella_files(n), & - rem_umbrella_files(perm(n + 1))) - end if ! imode.eq.MODE_FLOODING - - if (imode.ne.MODE_ANALYSIS) & - call umbrella_swap(rem_umbrellas(n), & - rem_umbrellas(perm(n + 1))) - end if ! n.gt.perm(n + 1) - exchange_partner = masterrank - end do - - deallocate(perm) - - ! adjust filenames/freqs/umbrellas - - monitor_file = rem_monitor_files(masterrank) - monitor_freq = rem_monitor_freqs(masterrank) - - if (imode.eq.MODE_FLOODING) then - snapshots_freq = rem_snapshots_freqs(masterrank) - snapshots_basename = rem_snapshots_basenames(masterrank) - umbrella_file = rem_umbrella_files(masterrank) - end if - - if (imode.ne.MODE_ANALYSIS) & - call umbrella_swap(umbrella, rem_umbrellas(masterrank)) - ! re-open MONITOR_UNIT after exchange (closed in on_sander_exit()) open (unit = MONITOR_UNIT, file = monitor_file, & iostat = error, form = 'FORMATTED', action = 'WRITE', & @@ -450,30 +380,18 @@ subroutine on_sander_init(mdin_unit, amass) 'could not open ''', trim(monitor_file), ''' file for writing' call terminate() end if - end if ! imode.ne.MODE_NONE NFE_MASTER_ONLY_END - if (imode.eq.MODE_ANALYSIS) then - call mpi_bcast(monitor_freq, 1, MPI_INTEGER, 0, commsander, error) - nfe_assert(error.eq.0) - end if - - return - + return ! return for REMD end if ! counter.gt.0 counter = counter + 1 NFE_MASTER_ONLY_BEGIN - if (multisander_rem().ne.0) then - nfe_assert(multisander_numgroup().gt.1) - exchange_partner = masterrank - n = rem_idx - else if (multisander_numgroup().gt.1) then + if (multisander_numgroup().gt.1) & n = masterrank + 1 - end if if (multisander_numgroup().gt.1) then write (unit = monitor_file, fmt = '(a,a,i3.3)') & @@ -749,6 +667,7 @@ subroutine on_sander_init(mdin_unit, amass) stat = error) allocate(all_n(multisander_numgroup()), & stat = error) + call amrset_gen(nfe_abmd_gen, ig+masterrank) end if ! selection_freq.gt.0 end if #endif /* NFE_ENABLE_BBMD */ @@ -803,6 +722,7 @@ subroutine on_sander_init(mdin_unit, amass) stat = error) allocate(all_n(multisander_numgroup()), & stat = error) + call amrset_gen(nfe_abmd_gen, ig+masterrank) end if ! selection_freq.gt.0 #endif /* NFE_ENABLE_BBMD */ ! Moradi end @@ -857,46 +777,9 @@ subroutine on_sander_init(mdin_unit, amass) ! print summary & return #ifdef MPI - if (multisander_rem().eq.0) then - LOG_UNIT = OUT_UNIT ! write to MDOUT - else - LOG_UNIT = REMLOG_UNIT - - if (masterrank.eq.0) then - open (unit = LOG_UNIT, file = REMLOG_FILE, iostat = error, & - form = 'FORMATTED', action = 'WRITE', status = 'REPLACE') - - if (error.ne.0) then - write (unit = ERR_UNIT, fmt = '(/a,a,a,a/)') NFE_ERROR, & - 'failed to open ''', trim(REMLOG_FILE), ''' for writing' - call terminate() - end if - write (unit = LOG_UNIT, fmt = '(80(''*''))') - close (unit = LOG_UNIT) - end if ! masterrank.eq.0 - - call cpus_enter(commmaster, 12345) - - open (unit = LOG_UNIT, file = REMLOG_FILE, & - iostat = error, form = 'FORMATTED', action = 'WRITE', & - position = 'APPEND', status = 'OLD') - - if (error.ne.0) then - write (unit = ERR_UNIT, fmt = '(/a,a,a,a/)') NFE_ERROR, & - 'could not open ''', trim(REMLOG_FILE), ''' file for writing' - call terminate() - end if - - write (unit = LOG_UNIT, fmt = & - '(/23x,a,'//pfmt(masterrank)//',a,'//pfmt(sander_temp0(), 3)//',a/)') & - 'REPLICA #', masterrank, ' (temp0 = ', sander_temp0(), ')' - write (unit = LOG_UNIT, fmt = '(1x,a,a,a)') & - 'MDIN = ''', trim(mdin_name), '''' - - end if -#else -# define LOG_UNIT OUT_UNIT + LOG_UNIT = OUT_UNIT ! write to MDOUT #endif + write (unit = LOG_UNIT, fmt = '(/a,a)') NFE_INFO, & '() () () () () () () () () () A. B. M. D. () () () () () () () () ()' write (unit = LOG_UNIT, fmt = '(a,/a,a)', advance = 'NO') & @@ -1068,13 +951,6 @@ subroutine on_sander_init(mdin_unit, amass) #ifdef MPI - if (multisander_rem().ne.0) then - write (unit = LOG_UNIT, fmt = '(/80(''*''))') - close (unit = LOG_UNIT) - call cpus_leave(commmaster, 12345) - call rem_postinit() ! allocates/populates rem_* arrays - end if - NFE_MASTER_ONLY_END return @@ -1097,6 +973,10 @@ subroutine rem_checks() nfe_assert(mastersize.gt.0) nfe_assert(masterrank.lt.mastersize) + ! For H-REMD and Multi-REMD, imode and ncolvar can vary among replicas + if (multisander_rem().eq.3 .or. multisander_rem().eq.-1) & + return + allocate(int_recv(mastersize), stat = error) if (error.ne.0) & NFE_OUT_OF_MEMORY @@ -1149,7 +1029,7 @@ end subroutine on_sander_exit ! Modified by M Moradi ! Driven ABMD -subroutine on_force(x, f, wdriven, udriven) +subroutine on_force(x, f, wdriven, udriven, pot) ! Moradi end use nfe_utils @@ -1170,6 +1050,7 @@ subroutine on_force(x, f, wdriven, udriven) NFE_REAL, intent(in) :: udriven ! Moradi end + NFE_REAL, intent(inout) :: pot #ifdef MPI # include "nfe-mpi.h" @@ -1181,17 +1062,14 @@ subroutine on_force(x, f, wdriven, udriven) character(len = SL + 16) :: snapshot integer :: n - logical :: real_mdstep if (imode.eq.MODE_NONE) & return - real_mdstep = (.not.multisander_initremd()).and.(sander_init().eq.4) - nfe_assert(ncolvars.gt.0) if (imode.eq.MODE_ANALYSIS) then - if (real_mdstep.and.mod(mdstep - 1, monitor_freq).eq.0) then + if (nfe_real_mdstep.and.mod(mdstep, monitor_freq).eq.0) then do n = 1, ncolvars instantaneous(n) = colvar_value(colvars(n), x) end do @@ -1215,12 +1093,16 @@ subroutine on_force(x, f, wdriven, udriven) NFE_MASTER_ONLY_BEGIN call umbrella_eval_vdv(umbrella, instantaneous, u_value, u_derivative) + pot = umbrella_eval_v(umbrella, instantaneous) NFE_MASTER_ONLY_END #ifdef MPI call mpi_bcast(u_derivative, ncolvars, & MPI_DOUBLE_PRECISION, 0, commsander, error) nfe_assert(error.eq.0) + call mpi_bcast(pot, 1, & + MPI_DOUBLE_PRECISION, 0, commsander, error) + nfe_assert(error.eq.0) #endif /* MPI */ ! FIXME: virial @@ -1228,12 +1110,9 @@ subroutine on_force(x, f, wdriven, udriven) call colvar_force(colvars(n), x, -u_derivative(n), f) end do - if (real_mdstep) then + if (nfe_real_mdstep) then NFE_MASTER_ONLY_BEGIN - - ! mdstep.ge.monitor_freq - 1 is to avoid the sample right after exchange - if ((mdstep + 1).ge.monitor_freq & - .and.mod(mdstep + 1, monitor_freq).eq.0) then + if (mod(mdstep, monitor_freq).eq.0) then if (imode.eq.MODE_FLOODING) then write (unit = MONITOR_UNIT, fmt = monitor_fmt) & sander_mdtime(), instantaneous(1:ncolvars), u_value @@ -1290,21 +1169,8 @@ subroutine on_force(x, f, wdriven, udriven) all_hills(n*(ncolvars + 1) + 1:), & all_hills((n + 1)*(ncolvars + 1))) end do - else if (multisander_rem().eq.1) then - do n = 0, multisander_numgroup() - 1 - if (n.eq.masterrank) then - call umbrella_hill(umbrella, & - all_hills(n*(ncolvars + 1) + 1:), & - all_hills((n + 1)*(ncolvars + 1))) - else - call umbrella_hill(rem_umbrellas(n), & - all_hills(n*(ncolvars + 1) + 1:), & - all_hills((n + 1)*(ncolvars + 1))) - end if ! n.eq.masterrank - end do else - continue - nfe_assert_not_reached() + call umbrella_hill(umbrella, instantaneous, alt) end if else #endif /* MPI */ @@ -1316,9 +1182,9 @@ subroutine on_force(x, f, wdriven, udriven) end if NFE_MASTER_ONLY_END - end if ! real_mdstep + end if ! nfe_real_mdstep -1 if (real_mdstep) & +1 if (nfe_real_mdstep) & mdstep = mdstep + 1 end subroutine on_force @@ -1388,7 +1254,6 @@ subroutine on_mdstep(x, v) if (((imode.eq.MODE_FLOODING).or.(imode.eq.MODE_UMBRELLA)).and.(selection_freq.gt.0) & .and.(multisander_numgroup().gt.1) & - .and.(.not.multisander_initremd()) & .and.(sander_init().eq.4)) then nfe_assert(ncolvars.gt.0) @@ -1434,7 +1299,7 @@ subroutine on_mdstep(x, v) call mpi_barrier(commmaster,error) allocate(all_n(multisander_numgroup()), stat = error) if (masterrank.eq.0) then - call amrand(my_rand) + call amrand_gen(nfe_abmd_gen, my_rand) n_tot = 0 nfe_assert(allocated(all_n)) all_n = 0 @@ -1443,7 +1308,7 @@ subroutine on_mdstep(x, v) selection_criterion = ZERO do n = 1, multisander_numgroup() my_n = int(my_rand+multisander_numgroup()*sum(all_w(1:n))/w_norm) - selection_criterion = selection_criterion + (all_w(n)/w_norm) & + selection_criterion = selection_criterion + (all_w(n)/w_norm) & * log(multisander_numgroup()*all_w(n)/w_norm) write (unit= LOG_UNIT , fmt =& '(a,a,'//pfmt(n)//',a,'//pfmt(all_w(n),6)//',a,'& @@ -1457,8 +1322,11 @@ subroutine on_mdstep(x, v) end if end do if (selection_epsilon.lt.ONE) then - nfe_assert(selection_criterion.ge.ZERO) - if (selection_criterion.ge.selection_epsilon*log(NFE_TO_REAL(multisander_numgroup()))) then + nfe_assert(selection_criterion.ge.-TINY) + if (abs(selection_criterion).lt.TINY) & + selection_criterion = ZERO + if (selection_criterion.ge.selection_epsilon* & + log(NFE_TO_REAL(multisander_numgroup()))) then write (unit= LOG_UNIT , fmt =& '(a,a,'//pfmt(selection_criterion,6)//',a,'& //pfmt(selection_epsilon*log(NFE_TO_REAL(multisander_numgroup())),6)//')')& @@ -1473,7 +1341,7 @@ subroutine on_mdstep(x, v) ' is below the threshold ', & selection_epsilon*log(NFE_TO_REAL(multisander_numgroup())),& NFE_INFO,'selection process will be stopped.',NFE_INFO - selection_freq = 0 + selection_freq = 0 end if end if end if @@ -1485,6 +1353,7 @@ subroutine on_mdstep(x, v) nfe_assert(error.eq.0) call mpi_barrier(commmaster,error) my_w = ZERO + if (masterrank+1.ne.all_n(masterrank+1)) then x(1:3*sander_natoms()) = & all_x((all_n(masterrank+1)-1)*3*sander_natoms()+1:all_n(masterrank+1)*3*sander_natoms()) diff --git AmberTools/src/sander/nfe-bbmd-ctxt.F90 AmberTools/src/sander/nfe-bbmd-ctxt.F90 index 4ca98e60b5..a675514db8 100644 --- AmberTools/src/sander/nfe-bbmd-ctxt.F90 +++ AmberTools/src/sander/nfe-bbmd-ctxt.F90 @@ -20,7 +20,7 @@ private integer, private, parameter :: MONITOR_UNIT = BBMD_MONITOR_UNIT integer, private, parameter :: CV_UNIT = BBMD_CV_UNIT -character(*), private, parameter :: SECTION = 'nfe_bbmd' +character(*), private, parameter :: SECTION = 'bbmd' character(*), private, parameter :: & DEFAULT_MONITOR_FILE = 'nfe-bbmd-monitor', & @@ -843,18 +843,32 @@ subroutine ctxt_bcast(self, masterroot, amass) call mpi_bcast(self%timescale, 1, & MPI_DOUBLE_PRECISION, masterroot, commmaster, error) nfe_assert(error.eq.0) - - call mpi_bcast(self%wt_umbrella_file, len(self%wt_umbrella_file), & + + call umbrella_bcast(self%umbrella, commmaster, masterroot) + + if (self%imode.eq.MODE_FLOODING) then + call mpi_bcast(self%wt_umbrella_file, len(self%wt_umbrella_file), & MPI_CHARACTER, masterroot, commmaster, error) - nfe_assert(error.eq.0) + nfe_assert(error.eq.0) - call mpi_bcast(self%pseudo, 1, & + call mpi_bcast(self%pseudo, 1, & MPI_DOUBLE_PRECISION, masterroot, commmaster, error) - nfe_assert(error.eq.0) + nfe_assert(error.eq.0) - call umbrella_bcast(self%umbrella, commmaster, masterroot) + call mpi_bcast(self%drivenu, 1, & + MPI_INTEGER, masterroot, commmaster, error) + nfe_assert(error.eq.0) + + call mpi_bcast(self%drivenw, 1, & + MPI_INTEGER, masterroot, commmaster, error) + nfe_assert(error.eq.0) - call umbrella_bcast(self%wt_umbrella, commmaster, masterroot) + call mpi_bcast(self%driven_cutoff, 1, & + MPI_DOUBLE_PRECISION, masterroot, commmaster, error) + nfe_assert(error.eq.0) + + call umbrella_bcast(self%wt_umbrella, commmaster, masterroot) + end if end if ! sanderrank.eq.0 @@ -934,7 +948,7 @@ end subroutine ctxt_bcast ! Modified by M Moradi ! Driven ABMD -subroutine ctxt_on_force(self, x, f, mdstep, wdriven, udriven) +subroutine ctxt_on_force(self, x, f, mdstep, wdriven, udriven, pot) ! Moradi end use nfe_utils @@ -958,6 +972,8 @@ subroutine ctxt_on_force(self, x, f, mdstep, wdriven, udriven) NFE_REAL, intent(in) :: wdriven NFE_REAL, intent(in) :: udriven ! Moradi end + + NFE_REAL, intent(inout) :: pot # include "nfe-mpi.h" @@ -968,19 +984,16 @@ subroutine ctxt_on_force(self, x, f, mdstep, wdriven, udriven) character(len = SL + 16) :: snapshot integer :: n, error - logical :: real_mdstep nfe_assert(self%initialized) if (self%imode.eq.MODE_NONE) & return - real_mdstep = (sander_init().eq.4) - nfe_assert(self%ncolvars.gt.0) if (self%imode.eq.MODE_ANALYSIS) then - if (real_mdstep.and.mod(mdstep, self%monitor_freq).eq.0) then + if (nfe_real_mdstep.and.mod(mdstep, self%monitor_freq).eq.0) then do n = 1, self%ncolvars instantaneous(n) = colvar_value(self%colvars(n), x) end do @@ -1003,20 +1016,25 @@ subroutine ctxt_on_force(self, x, f, mdstep, wdriven, udriven) instantaneous(n) = colvar_value(self%colvars(n), x) end do - if (sanderrank.eq.0) & + if (sanderrank.eq.0) then call umbrella_eval_vdv(self%umbrella, instantaneous, & u_value, u_derivative) + pot = umbrella_eval_v(self%umbrella, instantaneous) + end if call mpi_bcast(u_derivative, self%ncolvars, & MPI_DOUBLE_PRECISION, 0, commsander, error) nfe_assert(error.eq.0) + call mpi_bcast(pot, 1, & + MPI_DOUBLE_PRECISION, 0, commsander, error) + nfe_assert(error.eq.0) ! FIXME: virial do n = 1, self%ncolvars call colvar_force(self%colvars(n), x, -u_derivative(n), f) end do - if (.not.real_mdstep.or.sanderrank.ne.0) & + if (.not.nfe_real_mdstep.or.sanderrank.ne.0) & return nfe_assert(self%imode.eq.MODE_UMBRELLA.or.self%imode.eq.MODE_FLOODING) diff --git AmberTools/src/sander/nfe-bbmd-hooks.F90 AmberTools/src/sander/nfe-bbmd-hooks.F90 index 46988586ee..d445b60519 100644 --- AmberTools/src/sander/nfe-bbmd-hooks.F90 +++ AmberTools/src/sander/nfe-bbmd-hooks.F90 @@ -5,6 +5,12 @@ ! Bizarrely Biased MD ! !---------------------! +!------------------------------------------------------------------ +! Updated in Sep. 18, since the compatible H-REMD is implemented by +! F. Pan (with -rem 3), this module seems redundant, but we still +! keep it for records. +!------------------------------------------------------------------ + module nfe_bbmd_hooks #ifdef NFE_ENABLE_BBMD @@ -24,7 +30,7 @@ public :: on_mdwrit !<>< ><> <>< ><> <>< ><> <>< ><> <>< ><> <>< ><> <>< ><> <>< ><> <>< ><> <>< ><> -character(*), private, parameter :: SECTION = 'nfe_bbmd' +character(*), private, parameter :: SECTION = 'bbmd' integer, private, save :: active = 0 ! integer for MPI @@ -330,7 +336,7 @@ end subroutine on_sander_exit ! Modified by M Moradi ! Driven ABMD -subroutine on_force(x, f, work, udr) +subroutine on_force(x, f, work, udr, pot) ! Moradi end NFE_USE_AFAILED @@ -349,6 +355,8 @@ subroutine on_force(x, f, work, udr) NFE_REAL, intent(in) :: work NFE_REAL, intent(in) :: udr ! Moradi end + + NFE_REAL, intent(inout) :: pot # include "nfe-mpi.h" @@ -364,7 +372,7 @@ subroutine on_force(x, f, work, udr) nfe_assert(allocated(contexts)) nfe_assert(allocated(permutation)) - call ctxt_on_force(contexts(current), x, f, mdstep, work, udr) + call ctxt_on_force(contexts(current), x, f, mdstep, work, udr, pot) nfe_assert(partner.lt.0) @@ -452,7 +460,7 @@ subroutine on_mdstep(E_p, v, ekmh) # include "nfe-mpi.h" NFE_REAL :: v_scale - NFE_REAL :: partner_E_p, temp0, partner_temp0 + NFE_REAL :: E_px, partner_E_px, temp0, partner_temp0 NFE_REAL :: beta_m, beta_o, delta, random_number integer :: error, exchange, n @@ -468,6 +476,10 @@ subroutine on_mdstep(E_p, v, ekmh) mdstep = mdstep + 1 + ! added by F Pan, since we already include the potential contribution + ! from bbmd in E_p, we need to deduct it + E_px = E_p - nfe_pot_ene%bbmd + if (mod(mdstep, exchange_freq).ne.0) then if (mdstep.eq.sander_nstlim()) & goto 2 ! update_log() @@ -492,12 +504,12 @@ subroutine on_mdstep(E_p, v, ekmh) ! get partner's E_p if (masterrank.lt.partner_masterrank) then - call mpi_recv(partner_E_p, 1, MPI_DOUBLE_PRECISION, & + call mpi_recv(partner_E_px, 1, MPI_DOUBLE_PRECISION, & partner_masterrank, mdstep, commmaster, & MPI_STATUS_IGNORE, error) nfe_assert(error.eq.0) else - call mpi_send(E_p, 1, MPI_DOUBLE_PRECISION, & + call mpi_send(E_px, 1, MPI_DOUBLE_PRECISION, & partner_masterrank, mdstep, commmaster, error) nfe_assert(error.eq.0) end if @@ -516,7 +528,7 @@ subroutine on_mdstep(E_p, v, ekmh) beta_m = 503.01D0/temp0 beta_o = 503.01D0/partner_temp0 - delta = (beta_o - beta_m)*(E_p - partner_E_p) & + delta = (beta_o - beta_m)*(E_px - partner_E_px) & + beta_m*(U_mo - U_mm) - beta_o*(U_oo - U_om) if (delta.lt.ZERO) then diff --git AmberTools/src/sander/nfe-pmd-hooks.F90 AmberTools/src/sander/nfe-pmd-hooks.F90 index 5c107f52fd..a753c73fff 100644 --- AmberTools/src/sander/nfe-pmd-hooks.F90 +++ AmberTools/src/sander/nfe-pmd-hooks.F90 @@ -8,18 +8,16 @@ module nfe_pmd_hooks use nfe_constants, only : SL => STRING_LENGTH, PMD_OUTPUT_UNIT, PMD_CV_UNIT use nfe_colvar_type, only : colvar_t -#ifdef MPI -use nfe_constants, only : PMD_REMLOG_UNIT -#endif /* MPI */ - implicit none private +! old REMD subroutines, not used now ------ #ifdef MPI public :: on_delta public :: on_exchange #endif /* MPI */ +! ----------------------------------------- public :: on_multisander_exit @@ -33,17 +31,11 @@ public :: on_force integer, private, parameter :: pmd_UNIT = PMD_OUTPUT_UNIT integer, private, parameter :: CV_UNIT = PMD_CV_UNIT -character(*), private, parameter :: SECTION = 'nfe_pmd' character(*), private, parameter :: DEFAULT_OUTPUT_FILE = 'nfe-pmd' character(*), private, parameter :: DEFAULT_CV_FILE = 'nfe-pmd-cv' integer, private, parameter :: DEFAULT_OUTPUT_FREQ = 50 -#ifdef MPI -character(SL), private, parameter :: REMLOG_FILE = 'nfe-pmd.log' -integer, private, parameter :: REMLOG_UNIT = PMD_REMLOG_UNIT -#endif /* MPI */ - !- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - integer, private, save :: ncolvars = 0 ! .gt.0 means "active" @@ -121,27 +113,31 @@ subroutine on_delta(o_masterrank, need_U_xx, U_mm, U_mo, U_om, U_oo) do n = 1, ncolvars if (cv_inst(n).le.a_position(4*n-3)) then - U_m(1) = a_strength(2*n-1)*colvar_difference(cv(n),a_position(4*n-3),a_position(4*n-2))*cv_inst(n) + U_m(1) = U_m(1)+a_strength(2*n-1)*colvar_difference(cv(n),a_position(4*n-3),a_position(4*n-2))*cv_inst(n) + & + 0.5*a_strength(2*n-1)*(a_position(4*n-2)**2-a_position(4*n-3)**2) else if (cv_inst(n).le.a_position(4*n-2)) then - U_m(1) = a_strength(2*n-1)*colvar_difference(cv(n),cv_inst(n),a_position(4*n-2))**2/2 + U_m(1) = U_m(1)+a_strength(2*n-1)*colvar_difference(cv(n),cv_inst(n),a_position(4*n-2))**2/2 else if (cv_inst(n).le.a_position(4*n-1)) then U_m(1) = 0.0 else if (cv_inst(n).le.a_position(4*n)) then - U_m(1) = a_strength(2*n)*colvar_difference(cv(n),cv_inst(n),a_position(4*n-1))**2/2 + U_m(1) = U_m(1)+a_strength(2*n)*colvar_difference(cv(n),cv_inst(n),a_position(4*n-1))**2/2 else - U_m(1) = a_strength(2*n)*colvar_difference(cv(n), a_position(4*n), a_position(4*n-1))*cv_inst(n) + U_m(1) = U_m(1)+a_strength(2*n)*colvar_difference(cv(n), a_position(4*n), a_position(4*n-1))*cv_inst(n) + & + 0.5*a_strength(2*n)*(a_position(4*n-1)**2-a_position(4*n)**2) end if if (f_cv(n).le.a_position(4*n-3)) then - U_m(2) = a_strength(2*n-1)*colvar_difference(cv(n),a_position(4*n-3),a_position(4*n-2))*f_cv(n) + U_m(2) = U_m(2)+a_strength(2*n-1)*colvar_difference(cv(n),a_position(4*n-3),a_position(4*n-2))*f_cv(n) + & + 0.5*a_strength(2*n-1)*(a_position(4*n-2)**2-a_position(4*n-3)**2) else if (f_cv(n).le.a_position(4*n-2)) then - U_m(2) = a_strength(2*n-1)*colvar_difference(cv(n),f_cv(n),a_position(4*n-2))**2/2 + U_m(2) = U_m(2)+a_strength(2*n-1)*colvar_difference(cv(n),f_cv(n),a_position(4*n-2))**2/2 else if (f_cv(n).le.a_position(4*n-1)) then U_m(2) = 0.0 else if (f_cv(n).le.a_position(4*n)) then - U_m(2) = a_strength(2*n)*colvar_difference(cv(n),f_cv(n),a_position(4*n-1))**2/2 + U_m(2) = U_m(2)+a_strength(2*n)*colvar_difference(cv(n),f_cv(n),a_position(4*n-1))**2/2 else - U_m(2) = a_strength(2*n)*colvar_difference(cv(n), a_position(4*n),a_position(4*n-1))*f_cv(n) + U_m(2) = U_m(2)+a_strength(2*n)*colvar_difference(cv(n), a_position(4*n),a_position(4*n-1))*f_cv(n) + & + 0.5*a_strength(2*n)*(a_position(4*n-1)**2-a_position(4*n)**2) end if end do @@ -219,9 +215,6 @@ end subroutine on_exchange subroutine on_multisander_exit() use nfe_colvar, only : colvar_cleanup -# ifdef MPI - use nfe_sander_proxy, only : multisander_rem -# endif /* MPI */ implicit none @@ -237,10 +230,6 @@ subroutine on_multisander_exit() NFE_MASTER_ONLY_BEGIN nullify(a_position, a_strength) deallocate(anchor) -# ifdef MPI - if (multisander_rem().ne.0) & - deallocate(o_anchor) -# endif /* MPI */ NFE_MASTER_ONLY_END end if @@ -251,11 +240,7 @@ end subroutine on_multisander_exit !- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#ifdef MPI -subroutine on_sander_init(mdin_name, mdin_unit, amass, rem_idx) -#else subroutine on_sander_init(mdin_unit, amass) -#endif /* MPI */ use nfe_utils use nfe_colvar @@ -269,18 +254,13 @@ subroutine on_sander_init(mdin_unit, amass) NFE_REAL, intent(in) :: amass(*) -# ifdef MPI - integer, intent(in) :: rem_idx - character(SL), intent(in) :: mdin_name -# endif /* MPI */ - integer :: n, error, ifind character(80) :: buf # ifdef MPI logical, save :: first_time = .true. - integer :: LOG_UNIT # endif /* MPI */ + integer :: LOG_UNIT # include "nfe-mpi.h" @@ -289,6 +269,7 @@ subroutine on_sander_init(mdin_unit, amass) if (.not.first_time) then nfe_assert(multisander_rem().ne.0) + NFE_MASTER_ONLY_BEGIN if (ncolvars.gt.0) then ! re-open pmd_UNIT after exchange (closed in on_sander_exit()) @@ -303,6 +284,7 @@ subroutine on_sander_init(mdin_unit, amass) end if end if ! ncolvars.gt.0 NFE_MASTER_ONLY_END + return end if @@ -321,14 +303,15 @@ subroutine on_sander_init(mdin_unit, amass) ! output # ifdef MPI - if (multisander_rem().ne.0) then - write (unit = output_file, fmt = '(a,a,i3.3,a)') & - DEFAULT_OUTPUT_FILE, '.', rem_idx, '.txt' - else + if (multisander_numgroup().gt.1) then + n = masterrank + 1 + write (unit = output_file, fmt = '(a,a,i3.3,a)') & + DEFAULT_OUTPUT_FILE, '.', n, '.dat' + else # endif /* MPI */ - output_file = DEFAULT_OUTPUT_FILE//'.txt' + output_file = DEFAULT_OUTPUT_FILE//'.dat' # ifdef MPI - end if ! multisander_rem().ne.0 + end if # endif /* MPI */ rewind(mdin_unit) @@ -429,7 +412,7 @@ subroutine on_sander_init(mdin_unit, amass) & '//pfmt(a_position(4*n-2), 6)//',a,'//pfmt(a_position(4*n-1), 6)//',a, & & '//pfmt(a_position(4*n), 6)//', /a,'//pfmt(a_strength(2*n-1), 6)//',a, & & '//pfmt(a_strength(2*n), 6)//', a)' ) & - '# << anchor(', n, ') : position = ', a_position(4*n-3), ',',a_position(4*n-2),', ',& + '# << anchor(', n, ') : position = ', a_position(4*n-3), ', ',a_position(4*n-2),', ',& a_position(4*n-1),', ',a_position(4*n),& '# strength = ', a_strength(2*n-1),', ', a_strength(2*n), ' >>' end do @@ -444,50 +427,7 @@ subroutine on_sander_init(mdin_unit, amass) ! print summary & we'r done -# ifdef MPI - if (multisander_rem().eq.0) then - LOG_UNIT = OUT_UNIT ! write to MDOUT - else - allocate(o_anchor(6*ncolvars), stat = error) - if (error.ne.0) & - NFE_OUT_OF_MEMORY - - LOG_UNIT = REMLOG_UNIT - - if (masterrank.eq.0) then - open (unit = LOG_UNIT, file = REMLOG_FILE, iostat = error, & - form = 'FORMATTED', action = 'WRITE', status = 'REPLACE') - - if (error.ne.0) then - write (unit = ERR_UNIT, fmt = '(/a,a,a,a/)') NFE_ERROR, & - 'failed to open ''', trim(REMLOG_FILE), ''' for writing' - call terminate() - end if - write (unit = LOG_UNIT, fmt = '(80(''*''))') - close (unit = LOG_UNIT) - end if ! masterrank.eq.0 - - call cpus_enter(commmaster, 123456) - - open (unit = LOG_UNIT, file = REMLOG_FILE, & - iostat = error, form = 'FORMATTED', action = 'WRITE', & - position = 'APPEND', status = 'OLD') - - if (error.ne.0) then - write (unit = ERR_UNIT, fmt = '(/a,a,a,a/)') NFE_ERROR, & - 'could not open ''', trim(REMLOG_FILE), ''' file for writing' - call terminate() - end if - - write (unit = LOG_UNIT, fmt = '(/23x,a,'//pfmt(masterrank)//',a,f7.3,a/)') & - 'REPLICA #', masterrank, ' (temp0 = ', sander_temp0(), ')' - write (unit = LOG_UNIT, fmt = '(1x,a,a,a/)') & - 'MDIN = ''', trim(mdin_name), '''' - - end if ! multisander_rem().ne.0 -# else -# define LOG_UNIT OUT_UNIT -# endif + LOG_UNIT = OUT_UNIT ! write to MDOUT write (unit = LOG_UNIT, fmt = '(a,a)') NFE_INFO, & '~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~' @@ -506,7 +446,7 @@ subroutine on_sander_init(mdin_unit, amass) & '//pfmt(a_position(4*n-2), 6)//',a,'//pfmt(a_position(4*n-1), 6)//',a, & & '//pfmt(a_position(4*n), 6)//', /a,a, & & '//pfmt(a_strength(2*n-1),6)//',a,'//pfmt(a_strength(2*n), 6)//',a)' ) & - NFE_INFO, 'CV #', n, ' << anchor : position = ', a_position(4*n-3),',', & + NFE_INFO, 'CV #', n, ' << anchor : position = ', a_position(4*n-3),', ', & a_position(4*n-2),', ', a_position(4*n-1),', ',a_position(4*n), NFE_INFO,& ' strength = ', a_strength(2*n-1),', ', a_strength(2*n), ' >>' call colvar_print(cv(n), LOG_UNIT) @@ -516,14 +456,6 @@ subroutine on_sander_init(mdin_unit, amass) write (unit = LOG_UNIT, fmt = '(a,a/)') NFE_INFO, & '~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~' -# ifdef MPI - if (multisander_rem().ne.0) then - write (unit = LOG_UNIT, fmt = '(/80(''*''))') - close (unit = LOG_UNIT) - call cpus_leave(commmaster, 123456) - end if -# endif /* MPI */ - NFE_MASTER_ONLY_END return @@ -550,7 +482,7 @@ end subroutine on_sander_exit !- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -subroutine on_force(x, f) +subroutine on_force(x, f, pot) NFE_USE_AFAILED @@ -564,8 +496,8 @@ subroutine on_force(x, f) NFE_REAL, intent(in) :: x(*) NFE_REAL, intent(inout) :: f(*) + NFE_REAL, intent(inout) :: pot - logical :: real_mdstep integer :: n double precision :: fix_cv, apmean @@ -577,8 +509,6 @@ subroutine on_force(x, f) if (ncolvars.eq.0) & return - real_mdstep = (.not.multisander_initremd().and.sander_init().eq.4) - do n = 1, ncolvars cv_inst(n) = colvar_value(cv(n), x) end do @@ -601,14 +531,22 @@ subroutine on_force(x, f) if (fix_cv.le.a_position(4*n-3)) then f_cv(n) = -a_strength(2*n-1)*colvar_difference(cv(n),a_position(4*n-3),a_position(4*n-2)) + pot = pot + a_strength(2*n-1)* & + colvar_difference(cv(n),a_position(4*n-3),a_position(4*n-2))*fix_cv + & + 0.5*a_strength(2*n-1)*(a_position(4*n-2)**2-a_position(4*n-3)**2) else if (fix_cv.le.a_position(4*n-2)) then f_cv(n) = -a_strength(2*n-1)*colvar_difference(cv(n),cv_inst(n),a_position(4*n-2)) + pot = pot + a_strength(2*n-1)*colvar_difference(cv(n),cv_inst(n),a_position(4*n-2))**2/2 else if (fix_cv.le.a_position(4*n-1)) then f_cv(n) = 0.0 else if (fix_cv.le.a_position(4*n)) then f_cv(n) = -a_strength(2*n)*colvar_difference(cv(n),cv_inst(n),a_position(4*n-1)) + pot = pot + a_strength(2*n)*colvar_difference(cv(n),cv_inst(n),a_position(4*n-1))**2/2 else f_cv(n) = -a_strength(2*n)*colvar_difference(cv(n), a_position(4*n), a_position(4*n-1)) + pot = pot + a_strength(2*n)* & + colvar_difference(cv(n), a_position(4*n),a_position(4*n-1))*fix_cv + & + 0.5*a_strength(2*n)*(a_position(4*n-1)**2-a_position(4*n)**2) end if end do NFE_MASTER_ONLY_END @@ -617,6 +555,9 @@ subroutine on_force(x, f) call mpi_bcast(f_cv, ncolvars, & MPI_DOUBLE_PRECISION, 0, commsander, error) nfe_assert(error.eq.0) + call mpi_bcast(pot, 1, & + MPI_DOUBLE_PRECISION, 0, commsander, error) + nfe_assert(error.eq.0) # endif /* MPI */ ! FIXME: virial @@ -625,7 +566,7 @@ subroutine on_force(x, f) end do NFE_MASTER_ONLY_BEGIN - if (real_mdstep) then + if (nfe_real_mdstep) then if (mod(mdstep, output_freq).eq.0) then write (unit = pmd_UNIT, fmt = output_fmt) & @@ -635,7 +576,7 @@ subroutine on_force(x, f) mdstep = mdstep + 1 - end if ! real_mdstep + end if ! nfe_real_mdstep NFE_MASTER_ONLY_END end subroutine on_force diff --git AmberTools/src/sander/nfe-sander-hooks.F90 AmberTools/src/sander/nfe-sander-hooks.F90 index e452eee3c4..a9fa942494 100644 --- AmberTools/src/sander/nfe-sander-hooks.F90 +++ AmberTools/src/sander/nfe-sander-hooks.F90 @@ -21,10 +21,12 @@ private !----------------------------------------------------------------------------- ! remd.f +! old REMD subroutines, not used now -------- #ifdef MPI public :: on_delta public :: on_exchange #endif /* MPI */ +! ------------------------------------------- ! multisander.f public :: on_multisander_exit @@ -42,6 +44,7 @@ public :: on_force public :: on_mdwrit ! mdread.f +! old REMD subroutines, not used now #ifdef MPI public :: on_mdread1 #endif /* MPI */ @@ -52,7 +55,7 @@ public :: on_mdstep #endif /* NFE_ENABLE_BBMD */ !----------------------------------------------------------------------------- - +! old REMD subroutines and parms, not used now #ifdef MPI character(SL), private, save :: initial_mdin_name NFE_REAL, private, save :: initial_mdin_temp0 @@ -74,7 +77,6 @@ subroutine on_delta(o_masterrank, need_U_xx, U_mm, U_mo, U_om, U_oo) use nfe_pmd_hooks, only : pmd_on_delta => on_delta use nfe_abmd_hooks, only : abmd_on_delta => on_delta - use nfe_stsm_hooks, only : stsm_on_delta => on_delta implicit none @@ -90,7 +92,6 @@ subroutine on_delta(o_masterrank, need_U_xx, U_mm, U_mo, U_om, U_oo) call pmd_on_delta(o_masterrank, need_U_xx, U_mm, U_mo, U_om, U_oo) call abmd_on_delta(o_masterrank, need_U_xx, U_mm, U_mo, U_om, U_oo) - call stsm_on_delta(o_masterrank, need_U_xx, U_mm, U_mo, U_om, U_oo) end subroutine on_delta @@ -100,7 +101,6 @@ subroutine on_exchange(o_masterrank) use nfe_pmd_hooks, only : pmd_on_exchange => on_exchange use nfe_abmd_hooks, only : abmd_on_exchange => on_exchange - use nfe_stsm_hooks, only : stsm_on_exchange => on_exchange implicit none @@ -108,7 +108,6 @@ subroutine on_exchange(o_masterrank) call pmd_on_exchange(o_masterrank) call abmd_on_exchange(o_masterrank) - call stsm_on_exchange(o_masterrank) end subroutine on_exchange #endif /* MPI */ @@ -164,16 +163,12 @@ subroutine on_sander_init(ih, amass, acrds, rem) NFE_REAL, intent(in) :: acrds(*) integer, intent(in) :: rem + integer, save :: my_unit = 5 #ifdef MPI # include "nfe-mpi.h" logical, save :: first_call = .true. - integer, save :: my_unit = 5, my_idx = -1 - character(STRING_LENGTH), save :: my_mdin = '' - - integer :: ios - if (first_call) then #endif /* MPI */ call remember_rem(rem) @@ -181,26 +176,8 @@ subroutine on_sander_init(ih, amass, acrds, rem) NFE_MASTER_ONLY_BEGIN call remember_atom_names(ih) #ifdef MPI - if (multisander_rem().lt.3 .and. multisander_rem().gt.0) then - call rem_preinit(my_mdin, my_idx) - if (my_mdin.ne.sander_mdin_name()) then - my_unit = REM_MDIN_UNIT - open (unit = my_unit, file = my_mdin, iostat = ios, & - form = 'FORMATTED', action = 'READ', status = 'OLD') - if (ios > 0) then - write (unit = ERR_UNIT, fmt = '(/a,a,a,a/)') & - NFE_ERROR, 'failed to open ''', trim(my_mdin), & - ''' for reading' - call terminate() - end if - else - my_unit = 5 - end if ! my_mdin.ne.sander_mdin_name() - else - my_mdin = sander_mdin_name() - my_unit = 5 - end if ! multisander_rem().ne.0 NFE_MASTER_ONLY_END + first_call = .false. endif ! first_call #endif /* MPI */ @@ -208,21 +185,23 @@ subroutine on_sander_init(ih, amass, acrds, rem) #ifdef MPI if (multisander_rem().eq.0) & call smd_on_sander_init(my_unit, amass, acrds) +#else + call smd_on_sander_init(my_unit, amass, acrds) +#endif /* MPI */ - call pmd_on_sander_init(my_mdin, my_unit, amass, my_idx) - call abmd_on_sander_init(my_mdin, my_unit, amass, my_idx) - call stsm_on_sander_init(my_mdin, my_unit, amass, my_idx) + call pmd_on_sander_init(my_unit, amass) + call abmd_on_sander_init(my_unit, amass) #ifdef NFE_ENABLE_BBMD if (multisander_rem().eq.0.and.multisander_numgroup().gt.1) & call bbmd_on_sander_init(my_unit, amass) #endif /* NFE_ENABLE_BBMD */ +#ifdef MPI + if (multisander_rem().eq.0) & + call stsm_on_sander_init(my_unit, amass) #else - call smd_on_sander_init(5, amass, acrds) - call pmd_on_sander_init(5, amass) - call abmd_on_sander_init(5, amass) - call stsm_on_sander_init(5, amass) + call stsm_on_sander_init(my_unit, amass) #endif /* MPI */ end subroutine on_sander_init @@ -254,11 +233,12 @@ end subroutine on_sander_exit !----------------------------------------------------------------------------- -subroutine on_force(x, f) +subroutine on_force(x, f, pot) ! Modified by M Moradi use nfe_constants, only : ZERO ! Moradi end + use nfe_sander_proxy use nfe_smd_hooks, only : smd_on_force => on_force use nfe_pmd_hooks, only : pmd_on_force => on_force @@ -273,20 +253,30 @@ subroutine on_force(x, f) NFE_REAL, intent(in) :: x(*) NFE_REAL, intent(inout) :: f(*) + NFE_REAL, intent(inout) :: pot ! Modified by M Moradi ! for driven ABMD NFE_REAL :: wdriven = ZERO NFE_REAL :: udriven = ZERO - call smd_on_force(x, f, wdriven, udriven) - call pmd_on_force(x, f) - call abmd_on_force(x, f, wdriven, udriven) - call stsm_on_force(x, f) + nfe_pot_ene = null_nfe_pot_ene_rec + + call smd_on_force(x, f, wdriven, udriven, nfe_pot_ene%smd) + call pmd_on_force(x, f, nfe_pot_ene%pmd) + call abmd_on_force(x, f, wdriven, udriven, nfe_pot_ene%abmd) + call stsm_on_force(x, f, nfe_pot_ene%stsm) #ifdef NFE_ENABLE_BBMD - call bbmd_on_force(x, f, wdriven, udriven) + call bbmd_on_force(x, f, wdriven, udriven, nfe_pot_ene%bbmd) #endif /* NFE_ENABLE_BBMD */ ! Moradi end + + nfe_pot_ene%total = nfe_pot_ene%smd + nfe_pot_ene%pmd + & + nfe_pot_ene%abmd + nfe_pot_ene%bbmd + & + nfe_pot_ene%stsm + pot = nfe_pot_ene%total + + nfe_real_mdstep = .false. ! reset nfe_real_mdstep to false end subroutine on_force diff --git AmberTools/src/sander/nfe-sander-proxy.F90 AmberTools/src/sander/nfe-sander-proxy.F90 index d555e50227..a54bac0b76 100644 --- AmberTools/src/sander/nfe-sander-proxy.F90 +++ AmberTools/src/sander/nfe-sander-proxy.F90 @@ -60,6 +60,8 @@ private :: afailed public :: remember_rem public :: remember_initremd +public :: nfe_prt + integer, public, save :: infe = 0 integer, private, save :: saved_rem = -3212341 #ifdef MPI @@ -68,6 +70,29 @@ logical, private, save :: saved_initremd = .true. logical, private, save :: saved_initremd = .false. #endif /* MPI */ +! different from PMEMD, we set the default value of +! nfe_real_mdstep to false since force() is called +! much more often in sander +logical, public, save :: nfe_real_mdstep = .false. + +! NFE potential energy contribution, added by F. Pan +type nfe_pot_ene_rec + sequence + double precision :: smd + double precision :: pmd + double precision :: abmd + double precision :: bbmd + double precision :: stsm + double precision :: total ! restraint energy in NFE module +end type nfe_pot_ene_rec + +integer, parameter, public :: nfe_pot_ene_rec_size = 6 + +type(nfe_pot_ene_rec), parameter, public :: null_nfe_pot_ene_rec = & + nfe_pot_ene_rec(0.d0,0.d0,0.d0,0.d0,0.d0,0.d0) + +type(nfe_pot_ene_rec), public, save :: nfe_pot_ene = null_nfe_pot_ene_rec + !----------------------------------------------------------------------------- contains @@ -368,5 +393,23 @@ subroutine afailed(filename, lineno) end subroutine afailed #endif /* NFE_DISABLE_ASSERT */ +!----------------------------------------------------------------------------- + +subroutine nfe_prt(i) + implicit none + integer, intent(in) :: i + + if (infe .eq. 0) return + + write(i, 100) nfe_pot_ene%smd, nfe_pot_ene%pmd, nfe_pot_ene%abmd + write(i, 101) nfe_pot_ene%bbmd, nfe_pot_ene%stsm + write(i, 102) + return + +100 format(' NFE restraints: SMD :',f9.3,4x,'PMD : ',f9.3,4x, & + 'ABMD : ',f9.3) +101 format(20x,'BBMD :',f9.3,4x,'STSM : ',f9.3) +102 format(79('=')) +end subroutine nfe_prt end module nfe_sander_proxy diff --git AmberTools/src/sander/nfe-smd-hooks.F90 AmberTools/src/sander/nfe-smd-hooks.F90 index ef8619f2ad..98ba21c8b1 100644 --- AmberTools/src/sander/nfe-smd-hooks.F90 +++ AmberTools/src/sander/nfe-smd-hooks.F90 @@ -22,7 +22,6 @@ public :: on_force integer, private, parameter :: smd_UNIT = SMD_OUTPUT_UNIT integer, private, parameter :: CV_UNIT = SMD_CV_UNIT -character(*), private, parameter :: SECTION = 'nfe_smd' character(*), private, parameter :: DEFAULT_OUTPUT_FILE = 'nfe-smd.txt' character(*), private, parameter :: DEFAULT_CV_FILE = 'nfe-smd-cv' @@ -389,7 +388,7 @@ end subroutine on_sander_exit ! Modified by M Moradi ! for driven ABMD -subroutine on_force(x, f, wdriven, udriven) +subroutine on_force(x, f, wdriven, udriven, pot) NFE_USE_AFAILED @@ -405,9 +404,10 @@ subroutine on_force(x, f, wdriven, udriven) NFE_REAL, intent(out) :: wdriven NFE_REAL, intent(out) :: udriven + NFE_REAL, intent(inout) :: pot + ! Moradi end - logical :: real_mdstep integer :: n NFE_REAL :: position, dwork, f2, dcv, dharm @@ -422,7 +422,6 @@ subroutine on_force(x, f, wdriven, udriven) dwork = ZERO nfe_assert(multisander_rem().eq.0) - real_mdstep = (sander_init().eq.4) position = NFE_TO_REAL(mdstep)/NFE_TO_REAL(sander_nstlim()) @@ -435,14 +434,17 @@ subroutine on_force(x, f, wdriven, udriven) NFE_MASTER_ONLY_BEGIN udriven = ZERO do n = 1, ncolvars - dharm = cv(n)%harm - cv(n)%harm = mode_eval(cv(n)%harm_mode, cv(n)%harm_path, position) - dharm = cv(n)%harm - dharm - dcv = cv(n)%curr - cv(n)%curr = mode_eval(cv(n)%path_mode, cv(n)%cvar_path, position) - dcv = cv(n)%curr - dcv + dharm = mode_eval(cv(n)%harm_mode, cv(n)%harm_path, position) - & + cv(n)%harm + if (nfe_real_mdstep) & + cv(n)%harm = mode_eval(cv(n)%harm_mode, cv(n)%harm_path, position) + dcv = mode_eval(cv(n)%path_mode, cv(n)%cvar_path, position) - & + cv(n)%curr + if (nfe_real_mdstep) & + cv(n)%curr = mode_eval(cv(n)%path_mode, cv(n)%cvar_path, position) f2 = fcv_curr(n) fcv_curr(n) = cv(n)%harm*colvar_difference(cv(n)%parent,cv(n)%curr,cv(n)%inst) + pot = pot + cv(n)%harm*colvar_difference(cv(n)%parent,cv(n)%curr,cv(n)%inst)**2/2 f2 = (f2 + fcv_curr(n))/2 dwork = dwork + f2*dcv + dharm*& colvar_difference(cv(n)%parent,cv(n)%curr,cv(n)%inst)**2/2 @@ -456,6 +458,9 @@ subroutine on_force(x, f, wdriven, udriven) call mpi_bcast(fcv_curr, ncolvars, & MPI_DOUBLE_PRECISION, 0, commsander, error) nfe_assert(error.eq.0) + call mpi_bcast(pot, 1, & + MPI_DOUBLE_PRECISION, 0, commsander, error) + nfe_assert(error.eq.0) # endif /* MPI */ ! FIXME: virial @@ -464,7 +469,7 @@ subroutine on_force(x, f, wdriven, udriven) end do NFE_MASTER_ONLY_BEGIN - if (real_mdstep) then + if (nfe_real_mdstep) then if (mdstep.gt.0) & work = work + dwork @@ -490,7 +495,7 @@ subroutine on_force(x, f, wdriven, udriven) mdstep = mdstep + 1 - end if ! real_mdstep + end if ! nfe_real_mdstep NFE_MASTER_ONLY_END end subroutine on_force diff --git AmberTools/src/sander/nfe-stsm-hooks.F90 AmberTools/src/sander/nfe-stsm-hooks.F90 index 2ba417fa4e..8a15655ce0 100644 --- AmberTools/src/sander/nfe-stsm-hooks.F90 +++ AmberTools/src/sander/nfe-stsm-hooks.F90 @@ -8,19 +8,10 @@ module nfe_stsm_hooks use nfe_constants, only : SL => STRING_LENGTH, STSM_OUTPUT_UNIT, STSM_CV_UNIT use nfe_colvar_type, only : colvar_t -#ifdef MPI -use nfe_constants, only : STSM_REMLOG_UNIT -#endif /* MPI */ - implicit none private -#ifdef MPI -public :: on_delta -public :: on_exchange -#endif /* MPI */ - public :: on_multisander_exit public :: on_sander_init @@ -38,11 +29,6 @@ character(*), private, parameter :: DEFAULT_CV_FILE = 'nfe-stsm-cv' integer, private, parameter :: DEFAULT_OUTPUT_FREQ = 50 -#ifdef MPI -character(SL), private, parameter :: REMLOG_FILE = 'nfe-stsm.log' -integer, private, parameter :: REMLOG_UNIT = STSM_REMLOG_UNIT -#endif /* MPI */ - !- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - integer, private, save :: ncolvars = 0 ! .gt.0 means "active" @@ -99,10 +85,6 @@ character(SL), private, save :: report_centers = 'NONE' !- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#ifdef MPI -NFE_REAL, private, pointer, save :: o_anchor(:) => null() ! master -#endif /* MPI */ - namelist / stsm / image, repeats, equilibration, release, & smoothing, report_centers, & output_file, output_freq, cv_file @@ -113,133 +95,9 @@ contains !- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#ifdef MPI -subroutine on_delta(o_masterrank, need_U_xx, U_mm, U_mo, U_om, U_oo) - - use nfe_colvar, only : colvar_difference - use nfe_colvar, only : colvar_interpolate - use nfe_constants, only : ZERO - -# ifndef NFE_DISABLE_ASSERT - use nfe_utils - use nfe_sander_proxy -# endif /* NFE_DISABLE_ASSERT */ - - implicit none - - integer, intent(in) :: o_masterrank - logical, intent(in) :: need_U_xx - - NFE_REAL, intent(inout) :: U_mm, U_mo, U_om, U_oo - -# include "nfe-mpi.h" - - NFE_REAL :: U_o(2), U_m(2) - - integer :: n, error - - if (ncolvars.eq.0) & - return - - nfe_assert(multisander_rem().ne.0) - nfe_assert(sanderrank.eq.0) ! master - nfe_assert(commmaster.ne.mpi_comm_null) - - ! exchange cv_inst(:) with the partner [store partner values in f_cv] - call mpi_sendrecv & - (cv_inst, ncolvars, MPI_DOUBLE_PRECISION, o_masterrank, mdstep, & - f_cv, ncolvars, MPI_DOUBLE_PRECISION, o_masterrank, mdstep, & - commmaster, MPI_STATUS_IGNORE, error) - nfe_assert(error.eq.0) - - ! evaluate 'my' values - U_m(1) = ZERO ! U_mm = U_m(x_m) - U_m(2) = ZERO ! U_mo = U_m(x_o) - - do n = 1, ncolvars - U_m(1) = U_m(1) & - + a_strength(n)*colvar_difference(cv(n), cv_inst(n), a_position(n))**2/2 - U_m(2) = U_m(2) & - + a_strength(n)*colvar_difference(cv(n), f_cv(n), a_position(n))**2/2 - end do - - ! get partner's U_m? (i.e., U_o? in this replica) - call mpi_sendrecv & - (U_m, 2, MPI_DOUBLE_PRECISION, o_masterrank, mdstep, & - U_o, 2, MPI_DOUBLE_PRECISION, o_masterrank, mdstep, & - commmaster, MPI_STATUS_IGNORE, error) - nfe_assert(error.eq.0) - - if (need_U_xx) then - U_mm = U_mm + U_m(1) - U_mo = U_mo + U_m(2) - U_om = U_om + U_o(2) - U_oo = U_oo + U_o(1) - end if - -end subroutine on_delta - -!- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -subroutine on_exchange(o_masterrank) - -# ifndef NFE_DISABLE_ASSERT - use nfe_utils - use nfe_sander_proxy -# endif /* NFE_DISABLE_ASSERT */ - - implicit none - - integer, intent(in) :: o_masterrank - -# include "nfe-mpi.h" - - character(SL) :: o_output_file - integer :: o_output_freq, error - - if (ncolvars.eq.0) & - return - - nfe_assert(multisander_rem().ne.0) - nfe_assert(sanderrank.eq.0) ! master - nfe_assert(commmaster.ne.mpi_comm_null) ! master - - ! slow & naive - - call mpi_sendrecv(output_file, SL, MPI_CHARACTER, o_masterrank, 5, & - o_output_file, SL, MPI_CHARACTER, o_masterrank, 5, & - commmaster, MPI_STATUS_IGNORE, error) - nfe_assert(error.eq.0) - output_file = o_output_file - - call mpi_sendrecv(output_freq, 1, MPI_INTEGER, o_masterrank, 6, & - o_output_freq, 1, MPI_INTEGER, o_masterrank, 6, & - commmaster, MPI_STATUS_IGNORE, error) - nfe_assert(error.eq.0) - output_freq = o_output_freq - - nfe_assert(associated(anchor)) - nfe_assert(associated(o_anchor)) - - call mpi_sendrecv & - (anchor, 2*ncolvars, MPI_DOUBLE_PRECISION, o_masterrank, 7, & - o_anchor, 2*ncolvars, MPI_DOUBLE_PRECISION, o_masterrank, 7, & - commmaster, MPI_STATUS_IGNORE, error) - nfe_assert(error.eq.0) - - anchor(1:2*ncolvars) = o_anchor(1:2*ncolvars) - -end subroutine on_exchange -#endif /* MPI */ - -!- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - subroutine on_multisander_exit() use nfe_colvar, only : colvar_cleanup -# ifdef MPI - use nfe_sander_proxy, only : multisander_rem -# endif /* MPI */ implicit none @@ -252,13 +110,10 @@ subroutine on_multisander_exit() call colvar_cleanup(cv(n)) end do deallocate(cv, f_cv, cv_inst) + NFE_MASTER_ONLY_BEGIN nullify(a_position, a_strength) deallocate(anchor,all_cv,all_anchor,all_image) -# ifdef MPI - if (multisander_rem().ne.0) & - deallocate(o_anchor) -# endif /* MPI */ NFE_MASTER_ONLY_END end if @@ -269,11 +124,7 @@ end subroutine on_multisander_exit !- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#ifdef MPI -subroutine on_sander_init(mdin_name, mdin_unit, amass, rem_idx) -#else subroutine on_sander_init(mdin_unit, amass) -#endif /* MPI */ use nfe_utils use nfe_colvar @@ -288,59 +139,30 @@ subroutine on_sander_init(mdin_unit, amass) NFE_REAL, intent(in) :: amass(*) -# ifdef MPI - integer, intent(in) :: rem_idx - character(SL), intent(in) :: mdin_name -# endif /* MPI */ - integer :: n, error, ifind character(len = 80) :: buf -# ifdef MPI - logical, save :: first_time = .true. integer :: LOG_UNIT -# endif /* MPI */ - -# include "nfe-mpi.h" # ifdef MPI - nfe_assert(first_time.or.multisander_rem().ne.0) - - if (.not.first_time) then - nfe_assert(multisander_rem().ne.0) - NFE_MASTER_ONLY_BEGIN - if (ncolvars.gt.0) then - ! re-open stsm_UNIT after exchange (closed in on_sander_exit()) - open (unit = stsm_UNIT, file = output_file, & - iostat = error, form = 'FORMATTED', action = 'WRITE', & - position = 'APPEND', status = 'OLD') - - if (error.ne.0) then - write (unit = ERR_UNIT, fmt = '(/a,a,a,a/)') NFE_ERROR, & - 'could not open ''', trim(output_file), ''' file for writing' - call terminate() - end if - end if ! ncolvars.gt.0 - NFE_MASTER_ONLY_END - return - end if - - first_time = .false. +# include "nfe-mpi.h" + nfe_assert(multisander_rem().eq.0) +# endif /* MPI */ NFE_MASTER_ONLY_BEGIN -# endif /* MPI */ nfe_assert(ncolvars.eq.0) # ifdef MPI - if (multisander_rem().ne.0) then - write (unit = output_file, fmt = '(a,a,i3.3,a)') & - DEFAULT_OUTPUT_FILE, '.', rem_idx, '.txt' + if (multisander_numgroup().gt.1) then + n = masterrank + 1 + write (unit = output_file, fmt = '(a,a,i3.3,a)') & + DEFAULT_OUTPUT_FILE, '.', n, '.dat' else # endif /* MPI */ - output_file = DEFAULT_OUTPUT_FILE//'.txt' + output_file = DEFAULT_OUTPUT_FILE//'.dat' # ifdef MPI - end if ! multisander_rem().ne.0 + end if # endif /* MPI */ rewind(mdin_unit) @@ -523,50 +345,7 @@ subroutine on_sander_init(mdin_unit, amass) ! print summary & we'r done -# ifdef MPI - if (multisander_rem().eq.0) then - LOG_UNIT = OUT_UNIT ! write to MDOUT - else - allocate(o_anchor(2*ncolvars), stat = error) - if (error.ne.0) & - NFE_OUT_OF_MEMORY - - LOG_UNIT = REMLOG_UNIT - - if (masterrank.eq.0) then - open (unit = LOG_UNIT, file = REMLOG_FILE, iostat = error, & - form = 'FORMATTED', action = 'WRITE', status = 'REPLACE') - - if (error.ne.0) then - write (unit = ERR_UNIT, fmt = '(/a,a,a,a/)') NFE_ERROR, & - 'failed to open ''', trim(REMLOG_FILE), ''' for writing' - call terminate() - end if - write (unit = LOG_UNIT, fmt = '(80(''*''))') - close (unit = LOG_UNIT) - end if ! masterrank.eq.0 - - call cpus_enter(commmaster, 123456) - - open (unit = LOG_UNIT, file = REMLOG_FILE, & - iostat = error, form = 'FORMATTED', action = 'WRITE', & - position = 'APPEND', status = 'OLD') - - if (error.ne.0) then - write (unit = ERR_UNIT, fmt = '(/a,a,a,a/)') NFE_ERROR, & - 'could not open ''', trim(REMLOG_FILE), ''' file for writing' - call terminate() - end if - - write (unit = LOG_UNIT, fmt = '(/23x,a,'//pfmt(masterrank)//',a,f7.3,a/)') & - 'REPLICA #', masterrank, ' (temp0 = ', sander_temp0(), ')' - write (unit = LOG_UNIT, fmt = '(1x,a,a,a/)') & - 'MDIN = ''', trim(mdin_name), '''' - - end if ! multisander_rem().ne.0 -# else -# define LOG_UNIT OUT_UNIT -# endif + LOG_UNIT = OUT_UNIT ! write to MDOUT write (unit = LOG_UNIT, fmt = '(a,a)') NFE_INFO, & '~~ ~~ ~~ ~~ ~~ STRING METHOD WITH SWARMS OF TRAJECTOTIES ~~ ~~ ~~ ~~ ~~' @@ -633,14 +412,6 @@ subroutine on_sander_init(mdin_unit, amass) write (unit = LOG_UNIT, fmt = '(a,a/)') NFE_INFO, & '~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~' -# ifdef MPI - if (multisander_rem().ne.0) then - write (unit = LOG_UNIT, fmt = '(/80(''*''))') - close (unit = LOG_UNIT) - call cpus_leave(commmaster, 123456) - end if -# endif /* MPI */ - NFE_MASTER_ONLY_END return @@ -667,7 +438,7 @@ end subroutine on_sander_exit !- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -subroutine on_force(x, f) +subroutine on_force(x, f, pot) NFE_USE_AFAILED @@ -681,8 +452,8 @@ subroutine on_force(x, f) NFE_REAL, intent(in) :: x(*) NFE_REAL, intent(inout) :: f(*) + NFE_REAL, intent(inout) :: pot - logical :: real_mdstep integer :: n # ifdef MPI @@ -704,8 +475,6 @@ subroutine on_force(x, f) if (ncolvars.eq.0) & return - real_mdstep = (.not.multisander_initremd().and.sander_init().eq.4) - do n = 1, ncolvars cv_inst(n) = colvar_value(cv(n), x) end do @@ -732,6 +501,7 @@ subroutine on_force(x, f) do n = 1, ncolvars f_cv(n) = & - a_strength(n)*colvar_difference(cv(n), cv_inst(n), a_position(n)) + pot = pot + a_strength(n)*colvar_difference(cv(n), cv_inst(n), a_position(n))**2/2 end do else f_cv(1:ncolvars) = 0.0 @@ -742,6 +512,9 @@ subroutine on_force(x, f) call mpi_bcast(f_cv, ncolvars, & MPI_DOUBLE_PRECISION, 0, commsander, error) nfe_assert(error.eq.0) + call mpi_bcast(pot, 1, & + MPI_DOUBLE_PRECISION, 0, commsander, error) + nfe_assert(error.eq.0) # endif /* MPI */ ! FIXME: virial @@ -750,7 +523,7 @@ subroutine on_force(x, f) end do NFE_MASTER_ONLY_BEGIN - if (real_mdstep) then + if (nfe_real_mdstep) then if (mod(mdstep, output_freq).eq.0) then write (unit = stsm_UNIT, fmt = output_fmt) & @@ -759,7 +532,7 @@ subroutine on_force(x, f) end if #ifdef MPI - NFE_MASTER_ONLY_BEGIN + NFE_MASTER_ONLY_BEGIN if (mod(mdstep,run_freq).eq.run_freq-1) then copy_index = (mdstep+1)/run_freq copy_index = mod(copy_index-1,num_repeats)+1 @@ -907,12 +680,13 @@ subroutine on_force(x, f) nfe_assert(allocated(cv_copy)) deallocate(cv_copy) end if - NFE_MASTER_ONLY_END + NFE_MASTER_ONLY_END #endif /* MPI */ mdstep = mdstep + 1 - end if ! real_mdstep + end if ! nfe_real_mdstep + NFE_MASTER_ONLY_END end subroutine on_force diff --git AmberTools/src/sander/remd.F90 AmberTools/src/sander/remd.F90 index c00fcee2ab..8e223ea225 100644 --- AmberTools/src/sander/remd.F90 +++ AmberTools/src/sander/remd.F90 @@ -1320,12 +1320,6 @@ subroutine subrem(rem_dim) use constants, only : TWO -#ifndef DISABLE_NFE - use nfe_sander_hooks, only: & - nfe_on_delta => on_delta, nfe_on_exchange => on_exchange - use nfe_sander_proxy, only: infe -#endif /* DISABLE_NFE */ - use sgld, only : isgld, tsgset, sgft, tempsg, temprxlf, epotlf, avgtlf, & avgeflf, avgefhf, avgcflf, avgcfhf, myscalsg, sgld_exchg, & tempsglookup, stagidlookup @@ -1368,10 +1362,6 @@ subroutine subrem(rem_dim) logical exchange -#ifndef DISABLE_NFE - _REAL_ U_mm, U_mo, U_om, U_oo, beta_m, beta_o -#endif /* DISABLE_NFE */ - ! --------------------- ! Initialize variables texchsuccess(:) = 0 @@ -1529,13 +1519,6 @@ subroutine subrem(rem_dim) end if end if ! (even/odd rank check) -#ifndef DISABLE_NFE - if ( infe == 1 ) then - call nfe_on_delta(o_repnum - 1, & - mod(myindex, 2) == 0, U_mm, U_mo, U_om, U_oo) - end if -#endif /* DISABLE_NFE */ - ! RREMD: If jumpright and this replica has highest T, then attempt an ! exchange with a random structure in the reservoir. ! Read coordinates from the file when we are in sander. @@ -1616,13 +1599,6 @@ subroutine subrem(rem_dim) / (my_remd_data%mytargettemp * o_temp0) end if ! REMD exchange calculation -#ifndef DISABLE_NFE - ! from Y.Sugita at al (JCP v=113 p=6042 year=2000) - beta_m = 503.01D0 / my_remd_data%mytargettemp - beta_o = 503.01D0 / o_temp0 - delta = delta + beta_m*(U_mo - U_mm) - beta_o*(U_oo - U_om) -#endif /* DISABLE_NFE */ - metrop = exp(-delta) if (rremd==3 .and. myindex==remd_size .and. jumpright(rem_dim)) & metrop = metrop * myclustersize / o_clustersize @@ -1746,12 +1722,6 @@ subroutine subrem(rem_dim) if(stagid /= o_stagid) & write(6,*) "Problem in exchange ID!", stagid, o_stagid end if - ! DAN ROE: No NFE for RREMD? -#ifndef DISABLE_NFE - if ( infe == 1 ) then - call nfe_on_exchange(o_repnum - 1) - end if -#endif /* DISABLE_NFE */ else ! RREMD highest replica my_remd_data%newtargettemp = my_remd_data%mytargettemp exchange = .true. diff --git AmberTools/src/sander/runmd.F90 AmberTools/src/sander/runmd.F90 index b1b6cfe92f..82fadeef8c 100644 --- AmberTools/src/sander/runmd.F90 +++ AmberTools/src/sander/runmd.F90 @@ -55,8 +55,8 @@ subroutine runmd(xx, ix, ih, ipairs, x, winv, amass, f, v, vold, xr, xc, & #if !defined(DISABLE_NFE) && defined(NFE_ENABLE_BBMD) use nfe_sander_hooks, only : nfe_on_mdstep => on_mdstep - use nfe_sander_proxy, only : infe #endif + use nfe_sander_proxy, only : infe, nfe_real_mdstep, nfe_prt use molecule, only: n_iwrap_mask_atoms, iwrap_mask_atoms use cmd_vars, only: activate, file_pos_cmd, file_vel_cmd, nstep_cmd, & @@ -1241,6 +1241,7 @@ subroutine runmd(xx, ix, ih, ipairs, x, winv, amass, f, v, vold, xr, xc, & !--- END DIPOLE PRINTING CODE --- }}} if (nmropt > 0) call nmrptx(6) + if (infe == 1) call nfe_prt(6) call amflsh(7) end if if (abfqmmm_param%abfqmmm == 1 .and. abfqmmm_param%system == 1) then @@ -1657,6 +1658,7 @@ subroutine runmd(xx, ix, ih, ipairs, x, winv, amass, f, v, vold, xr, xc, & npbstep = nstep iprint = 0 if (nstep == 0 .or. nstep+1 == nstlim) iprint = 1 + if (rem .eq. 0 .or. mdloop .gt. 0) nfe_real_mdstep = .True. if (sebomd_obj%do_sebomd) then ! Write down atomic charges and density matrix if needed @@ -4390,6 +4392,7 @@ subroutine runmd(xx, ix, ih, ipairs, x, winv, amass, f, v, vold, xr, xc, & ! End of dipole printing if (nmropt > 0) call nmrptx(6) + if (infe > 0) call nfe_prt(6) if (itgtmd == 2) then emtmd = 0.0d0 call mtmdcall(emtmd, xx(lmtmd01), ix(imtmd02), x, f, ih(m04), & @@ -4532,7 +4535,15 @@ subroutine runmd(xx, ix, ih, ipairs, x, winv, amass, f, v, vold, xr, xc, & call trace_output_mpi_tally( ) call timer_stop(TIME_VERLET) #if !defined(DISABLE_NFE) && defined(NFE_ENABLE_BBMD) - if (infe == 1) call nfe_on_mdstep(ener%pot%tot, x, v, ekmh) + if (infe == 1) then + call xdist(x, xx(lfrctmp), natom) + call xdist(v, xx(lfrctmp), natom) + call nfe_on_mdstep(ener%pot%tot, x, v, ekmh) + vold(istart3:iend3) = v(istart3:iend3) + do im = 1, iscale + vold(nr3+im) = v(nr3+im) + end do + end if #endif /* DISABLE_NFE is NOT defined, but NFE_ENABLE_BBMD is */ ! RISM debug: {{{ diff --git test/nfe/abmd_ANALYSIS/run-pmemd.sh test/nfe/abmd_ANALYSIS/run-pmemd.sh index 355e4f1aed..1e6605e063 100755 --- test/nfe/abmd_ANALYSIS/run-pmemd.sh +++ test/nfe/abmd_ANALYSIS/run-pmemd.sh @@ -38,7 +38,7 @@ cp -p ../inpcrd.4 ./inpcrd # run SANDER # -${SANDER_CMD} > sander.out 2>&1 +${SANDER_CMD} -O > sander.out 2>&1 ../../dacdif -t 1 save.pmemd/mdout mdout ../../dacdif -t 1 save.pmemd/monitor.txt monitor.txt diff --git test/nfe/abmd_ANALYSIS/run-sander.sh test/nfe/abmd_ANALYSIS/run-sander.sh index 2f1e761e55..519107e22a 100755 --- test/nfe/abmd_ANALYSIS/run-sander.sh +++ test/nfe/abmd_ANALYSIS/run-sander.sh @@ -16,7 +16,7 @@ if test $? -ne 0; then exit 0; fi -set_SANDER sander +set_SANDER sander.MPI set_SANDER_CMD 1 JUNK="mdout mdinfo restrt monitor.txt inpcrd prmtop sander.out" diff --git test/nfe/abmd_ANALYSIS/save.pmemd/mdout test/nfe/abmd_ANALYSIS/save.pmemd/mdout index 1eace82001..05b3d41c03 100644 --- test/nfe/abmd_ANALYSIS/save.pmemd/mdout +++ test/nfe/abmd_ANALYSIS/save.pmemd/mdout @@ -1,15 +1,17 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 06/07/2016 at 18:13:50 +| Run on 09/13/2018 at 17:46:41 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/abmd_ANALYSIS -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abmd_ANALYSIS +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output File Assignments: | MDIN: mdin @@ -35,7 +37,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -46,6 +48,7 @@ File Assignments: / +| irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: @@ -160,12 +163,12 @@ NGLY Forcing neutrality... | Dynamic Memory, Types Used: -| Reals 910539 -| Integers 194492 +| Reals 1107531 +| Integers 203748 -| Nonbonded Pairs Initial Allocation: 179150 +| Nonbonded Pairs Initial Allocation: 143320 -| Running AMBER/MPI version on 8 MPI task +| Running AMBER/MPI version on 10 MPI task -------------------------------------------------------------------------------- @@ -247,6 +250,9 @@ NGLY Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.15 PRESS = 0.0 Etot = -8329.3308 EKtot = 1917.1633 EPtot = -10246.4941 @@ -256,6 +262,9 @@ NGLY Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 Etot = -8320.0760 EKtot = 1879.6557 EPtot = -10199.7316 @@ -265,6 +274,9 @@ NGLY Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 Etot = -8311.9580 EKtot = 1892.0329 EPtot = -10203.9909 @@ -274,6 +286,9 @@ NGLY Ewald error estimate: 0.2632E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.80 PRESS = 0.0 Etot = -8313.5865 EKtot = 1908.6833 EPtot = -10222.2699 @@ -283,6 +298,9 @@ NGLY Ewald error estimate: 0.3060E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.89 PRESS = 0.0 Etot = -8308.1381 EKtot = 1947.1619 EPtot = -10255.3000 @@ -292,6 +310,9 @@ NGLY Ewald error estimate: 0.7442E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 296.00 PRESS = 0.0 Etot = -8312.3540 EKtot = 1871.9857 EPtot = -10184.3397 @@ -301,6 +322,9 @@ NGLY Ewald error estimate: 0.7106E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.08 PRESS = 0.0 Etot = -8316.3316 EKtot = 1897.7563 EPtot = -10214.0879 @@ -310,6 +334,9 @@ NGLY Ewald error estimate: 0.2671E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 298.95 PRESS = 0.0 Etot = -8320.6929 EKtot = 1890.6086 EPtot = -10211.3015 @@ -319,6 +346,9 @@ NGLY Ewald error estimate: 0.1563E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.28 PRESS = 0.0 Etot = -8323.4556 EKtot = 1930.6587 EPtot = -10254.1142 @@ -328,6 +358,9 @@ NGLY Ewald error estimate: 0.1030E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S @@ -360,73 +393,73 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.11 36.41 -| Nonbond 0.17 54.14 -| Bond 0.00 0.00 -| Angle 0.00 0.16 -| Dihedral 0.00 0.64 -| Shake 0.00 0.56 -| RunMD 0.02 7.76 -| Other 0.00 0.32 +| DataDistrib 0.06 35.40 +| Nonbond 0.08 45.69 +| Bond 0.00 0.06 +| Angle 0.00 0.06 +| Dihedral 0.00 0.69 +| Shake 0.00 0.12 +| RunMD 0.03 17.70 +| Other 0.00 0.29 | ------------------------------ -| Total 0.31 +| Total 0.17 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.32 -| Build List 0.02 5.32 +| Set Up Cit 0.00 0.23 +| Build List 0.01 4.86 | --------------------------------- -| Total 0.02 5.64 +| Total 0.01 5.09 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.11 34.21 -| Exclude Masked 0.00 0.44 -| Other 0.00 0.84 +| NonBonded Calc 0.04 25.91 +| Exclude Masked 0.00 0.58 +| Other 0.00 0.81 | --------------------------------- -| Total 0.11 35.49 +| Total 0.05 27.30 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.00 0.40 -| Grid Charges 0.00 0.84 -| Scalar Sum 0.01 2.48 -| Gradient Sum 0.01 1.64 -| FFT 0.02 7.32 +| 1D bspline 0.00 1.04 +| Grid Charges 0.00 0.87 +| Scalar Sum 0.00 1.91 +| Gradient Sum 0.00 1.79 +| FFT 0.01 7.29 | --------------------------------- -| Total 0.04 12.69 +| Total 0.02 12.90 | PME Load Balancing CPU Time, Average for All Tasks: | | Routine Sec % | ------------------------------------ | Atom Reassign 0.00 0.00 -| Image Reassign 0.00 0.12 -| FFT Reassign 0.00 0.16 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.52 | ------------------------------------ -| Total 0.00 0.28 +| Total 0.00 0.52 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.26 Per Step(ms) = 5.71 -| ns/day = 30.25 seconds/ns = 2856.04 +| Elapsed(s) = 0.13 Per Step(ms) = 2.95 +| ns/day = 58.64 seconds/ns = 1473.38 | | Average timings for all steps: -| Elapsed(s) = 0.32 Per Step(ms) = 6.44 -| ns/day = 26.83 seconds/ns = 3220.45 +| Elapsed(s) = 0.18 Per Step(ms) = 3.54 +| ns/day = 48.85 seconds/ns = 1768.75 | ----------------------------------------------------- -| Master Setup CPU time: 0.09 seconds -| Master NonSetup CPU time: 0.32 seconds -| Master Total CPU time: 0.41 seconds 0.00 hours +| Master Setup CPU time: 0.06 seconds +| Master NonSetup CPU time: 0.18 seconds +| Master Total CPU time: 0.23 seconds 0.00 hours | Master Setup wall time: 0 seconds -| Master NonSetup wall time: 1 seconds -| Master Total wall time: 1 seconds 0.00 hours +| Master NonSetup wall time: 0 seconds +| Master Total wall time: 0 seconds 0.00 hours diff --git test/nfe/abmd_ANALYSIS/save.sander/mdout test/nfe/abmd_ANALYSIS/save.sander/mdout index 8dbf6cb7ad..a51fcdffc1 100644 --- test/nfe/abmd_ANALYSIS/save.sander/mdout +++ test/nfe/abmd_ANALYSIS/save.sander/mdout @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/13/2016 at 18:28:07 +| Run on 09/01/2018 at 14:21:13 -| Executable path: /home/feng/git_feng/amber/bin/sander -| Working directory: /home/feng/git_feng/amber/test/nfe/abmd_ANALYSIS -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abmd_ANALYSIS +| Hostname: gaia.physics.ncsu.edu File Assignments: @@ -27,6 +27,14 @@ File Assignments: |RSTDIP: rstdip |INPTRA: inptraj +| REMLOG: rem.log +| REMTYPE: rem.type +| REMSTRIP: +| SAVEENE: saveene +|CLUSTERINF: cluster.info +| RESERVOIR: reserv/frame +| REMDDIM: + Here is the input file: @@ -37,7 +45,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -51,7 +59,7 @@ File Assignments: 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: +| Flags: MPI getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -69,13 +77,13 @@ File Assignments: | Memory Use Allocated -| Real 294892 +| Real 304361 | Hollerith 10444 | Integer 115557 -| Max Pairs 1047666 +| Max Pairs 261916 | nblistReal 37716 -| nblist Int 118089 -| Total 7644 kbytes +| nblist Int 105664 +| Total 4600 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -134,6 +142,9 @@ Ewald parameters: Ewald Coefficient = 0.34864 Interpolation order = 4 +| MPI Timing options: +| profile_mpi = 0 + -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- @@ -142,9 +153,14 @@ NGLY begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 1001 +| Atom division among processors: +| 0 392 785 1178 1568 1961 2354 2744 +| 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... +| Running AMBER/MPI version on 8 nodes + -------------------------------------------------------------------------------- 4. RESULTS @@ -212,7 +228,7 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 650668 +| Local SIZE OF NONBOND LIST = 84063 | TOTAL SIZE OF NONBOND LIST = 650668 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 @@ -223,6 +239,9 @@ NGLY Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.15 PRESS = 0.0 Etot = -8329.3308 EKtot = 1917.1633 EPtot = -10246.4941 @@ -232,6 +251,9 @@ NGLY Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 Etot = -8320.0760 EKtot = 1879.6557 EPtot = -10199.7316 @@ -241,6 +263,9 @@ NGLY Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 Etot = -8311.9580 EKtot = 1892.0329 EPtot = -10203.9909 @@ -250,6 +275,9 @@ NGLY Ewald error estimate: 0.2632E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.80 PRESS = 0.0 Etot = -8313.5865 EKtot = 1908.6833 EPtot = -10222.2699 @@ -259,6 +287,9 @@ NGLY Ewald error estimate: 0.3060E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.89 PRESS = 0.0 Etot = -8308.1381 EKtot = 1947.1619 EPtot = -10255.3000 @@ -268,6 +299,9 @@ NGLY Ewald error estimate: 0.7442E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 296.00 PRESS = 0.0 Etot = -8312.3540 EKtot = 1871.9857 EPtot = -10184.3397 @@ -277,6 +311,9 @@ NGLY Ewald error estimate: 0.7106E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.08 PRESS = 0.0 Etot = -8316.3316 EKtot = 1897.7563 EPtot = -10214.0879 @@ -286,6 +323,9 @@ NGLY Ewald error estimate: 0.2671E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 298.95 PRESS = 0.0 Etot = -8320.6929 EKtot = 1890.6086 EPtot = -10211.3015 @@ -295,6 +335,9 @@ NGLY Ewald error estimate: 0.1563E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.28 PRESS = 0.0 Etot = -8323.4556 EKtot = 1930.6587 EPtot = -10254.1142 @@ -304,6 +347,9 @@ NGLY Ewald error estimate: 0.1030E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 50 S T E P S @@ -333,51 +379,58 @@ NGLY 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.37% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.00 ( 0.23% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.29 (90.99% of List ) -| Other 0.03 ( 9.01% of List ) -| List time 0.32 (11.67% of Nonbo) -| Short_ene time 1.83 (99.18% of Direc) -| Other 0.02 ( 0.82% of Direc) -| Direct Ewald time 1.85 (77.04% of Ewald) -| Adjust Ewald time 0.01 ( 0.60% of Ewald) +| Build the list 0.02 (61.64% of List ) +| Other 0.01 (38.36% of List ) +| List time 0.04 (15.14% of Nonbo) +| Short_ene time 0.13 (95.17% of Direc) +| Other 0.01 ( 4.83% of Direc) +| Direct Ewald time 0.14 (68.02% of Ewald) +| Adjust Ewald time 0.00 ( 0.45% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 3.40% of Recip) -| Fill charge grid 0.04 ( 7.17% of Recip) -| Scalar sum 0.22 (41.54% of Recip) -| Grad sum 0.09 (16.13% of Recip) -| FFT time 0.17 (31.74% of Recip) -| Other 0.00 ( 0.02% of Recip) -| Recip Ewald time 0.53 (22.23% of Ewald) -| Force Adjust 0.00 ( 0.02% of Ewald) -| Virial junk 0.00 ( 0.04% of Ewald) -| Other 0.00 ( 0.06% of Ewald) -| Ewald time 2.40 (88.33% of Nonbo) -| Nonbond force 2.72 (99.39% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.46% of Force) -| Other 0.00 ( 0.15% of Force) -| Force time 2.73 (96.28% of Runmd) -| Shake time 0.02 ( 0.58% of Runmd) -| Verlet update time 0.09 ( 3.06% of Runmd) -| Other 0.00 ( 0.07% of Runmd) -| Runmd Time 2.84 (97.98% of Total) -| Other 0.05 ( 1.64% of Total) -| Total time 2.90 (100.0% of ALL ) +| Fill Bspline coeffs 0.00 ( 8.90% of Recip) +| Fill charge grid 0.00 ( 6.19% of Recip) +| Scalar sum 0.01 (26.22% of Recip) +| Grad sum 0.01 (12.90% of Recip) +| FFT back comm time 0.00 (15.98% of FFT t) +| Other 0.02 (84.02% of FFT t) +| FFT time 0.02 (42.49% of Recip) +| Other 0.00 ( 3.30% of Recip) +| Recip Ewald time 0.05 (26.61% of Ewald) +| Force Adjust 0.01 ( 4.34% of Ewald) +| Virial junk 0.00 ( 0.48% of Ewald) +| Start synchronizatio 0.00 ( 0.01% of Ewald) +| Other 0.00 ( 0.09% of Ewald) +| Ewald time 0.20 (84.85% of Nonbo) +| Other 0.00 ( 0.01% of Nonbo) +| Nonbond force 0.23 (97.99% of Force) +| Bond/Angle/Dihedral 0.00 ( 0.43% of Force) +| FRC Collect time 0.00 ( 1.07% of Force) +| Other 0.00 ( 0.51% of Force) +| Force time 0.24 (82.11% of Runmd) +| Shake time 0.00 ( 0.43% of Runmd) +| Verlet update time 0.05 (15.91% of Runmd) +| CRD distribute time 0.00 ( 0.58% of Runmd) +| Other 0.00 ( 0.96% of Runmd) +| Runmd Time 0.29 (84.95% of Total) +| Other 0.05 (14.81% of Total) +| Total time 0.34 (99.65% of ALL ) | Number of list builds : 5 -| Highest rstack allocated: 193099 -| Highest istack allocated: 3143 +| Highest rstack allocated: 41935 +| Highest istack allocated: 931 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 2.84 Per Step(ms) = 56.80 -| ns/day = 3.04 seconds/ns = 28399.90 +| Elapsed(s) = 0.29 Per Step(ms) = 5.84 +| ns/day = 29.56 seconds/ns = 2922.39 | ----------------------------------------------------- -| Job began at 18:28:07.254 on 06/13/2016 -| Setup done at 18:28:07.315 on 06/13/2016 -| Run done at 18:28:10.154 on 06/13/2016 -| wallclock() was called 2233 times +| Job began at 14:21:13.068 on 09/01/2018 +| Setup done at 14:21:13.121 on 09/01/2018 +| Run done at 14:21:13.413 on 09/01/2018 +| wallclock() was called 2783 times diff --git test/nfe/abmd_FLOODING/save.pmemd/mdout test/nfe/abmd_FLOODING/save.pmemd/mdout index 8234ec0b8d..9f690e9191 100644 --- test/nfe/abmd_FLOODING/save.pmemd/mdout +++ test/nfe/abmd_FLOODING/save.pmemd/mdout @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 06/03/2016 at 14:36:59 +| Run on 09/05/2018 at 13:06:55 -| Executable path: /home/feng/git_feng/amber/bin/pmemd -| Working directory: /home/feng/git_feng/amber/test/nfe/abmd_FLOODING -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abmd_FLOODING +| Hostname: gaia.physics.ncsu.edu File Assignments: | MDIN: mdin @@ -22,6 +22,7 @@ File Assignments: | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo +|LOGFILE: logfile | MDFRC: mdfrc @@ -34,7 +35,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -55,9 +56,11 @@ File Assignments: / +| irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: +| MPI | PUBFFT | BINTRAJ | EMIL @@ -147,6 +150,13 @@ Ewald parameters: Ewald Coefficient = 0.34864 Interpolation order = 4 +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- @@ -161,11 +171,14 @@ NGLY Forcing neutrality... | Dynamic Memory, Types Used: -| Reals 202260 -| Integers 79073 +| Reals 239932 +| Integers 206014 + +| Nonbonded Pairs Initial Allocation: 179151 -| Nonbonded Pairs Initial Allocation: 524959 +| Running AMBER/MPI version on 4 MPI task + -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- @@ -242,109 +255,150 @@ NGLY NFE : NFE : well-tempered ABMD: NFE : pseudo-temperature = 10000.000000 - NFE : wt_umbrella_file = wt_umbrella.nc + NFE : wt_umbrella_file = wt_umbrella.nc NFE : NFE : () () () () () () () () () () () () () () () () () () () () () () () () NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.4834 EKtot = 1914.1823 EPtot = -10235.6657 + Etot = -8321.4754 EKtot = 1914.1823 EPtot = -10235.6577 BOND = 19.0733 ANGLE = 63.5926 DIHED = 72.6962 1-4 NB = 31.9325 1-4 EEL = 541.0002 VDWAALS = 1297.2732 - EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10235.6657 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.15 PRESS = 0.0 - Etot = -8329.3307 EKtot = 1917.1634 EPtot = -10246.4941 + Etot = -8329.3128 EKtot = 1917.1634 EPtot = -10246.4762 BOND = 25.2746 ANGLE = 68.1064 DIHED = 73.1044 1-4 NB = 34.0179 1-4 EEL = 541.6437 VDWAALS = 1326.2609 - EELEC = -12314.9020 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9020 EHBOND = 0.0000 RESTRAINT = 0.0179 + EAMBER (non-restraint) = -10246.4941 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 - Etot = -8320.0759 EKtot = 1879.6557 EPtot = -10199.7316 + Etot = -8320.0480 EKtot = 1879.6557 EPtot = -10199.7037 BOND = 25.7310 ANGLE = 67.7043 DIHED = 76.2867 1-4 NB = 31.4947 1-4 EEL = 535.0451 VDWAALS = 1359.5170 - EELEC = -12295.5104 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12295.5104 EHBOND = 0.0000 RESTRAINT = 0.0279 + EAMBER (non-restraint) = -10199.7316 Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.028 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 - Etot = -8311.9580 EKtot = 1892.0330 EPtot = -10203.9910 + Etot = -8311.9201 EKtot = 1892.0330 EPtot = -10203.9531 BOND = 32.8306 ANGLE = 68.2449 DIHED = 72.8985 1-4 NB = 28.3900 1-4 EEL = 536.4113 VDWAALS = 1387.0681 - EELEC = -12329.8344 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12329.8344 EHBOND = 0.0000 RESTRAINT = 0.0379 + EAMBER (non-restraint) = -10203.9910 Ewald error estimate: 0.2632E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.038 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.80 PRESS = 0.0 - Etot = -8313.5864 EKtot = 1908.6834 EPtot = -10222.2699 + Etot = -8313.5386 EKtot = 1908.6834 EPtot = -10222.2220 BOND = 35.4463 ANGLE = 70.8435 DIHED = 73.4767 1-4 NB = 28.8885 1-4 EEL = 538.8834 VDWAALS = 1406.8392 - EELEC = -12376.6474 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12376.6474 EHBOND = 0.0000 RESTRAINT = 0.0478 + EAMBER (non-restraint) = -10222.2699 Ewald error estimate: 0.3060E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.048 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.89 PRESS = 0.0 - Etot = -8308.1379 EKtot = 1947.1620 EPtot = -10255.2999 + Etot = -8308.0802 EKtot = 1947.1620 EPtot = -10255.2423 BOND = 32.8607 ANGLE = 64.4499 DIHED = 74.4288 1-4 NB = 30.2039 1-4 EEL = 534.5190 VDWAALS = 1408.1037 - EELEC = -12399.8659 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12399.8659 EHBOND = 0.0000 RESTRAINT = 0.0577 + EAMBER (non-restraint) = -10255.2999 Ewald error estimate: 0.7442E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.058 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 296.00 PRESS = 0.0 - Etot = -8312.3539 EKtot = 1871.9858 EPtot = -10184.3397 + Etot = -8312.2862 EKtot = 1871.9858 EPtot = -10184.2720 BOND = 23.7478 ANGLE = 70.9252 DIHED = 73.5149 1-4 NB = 30.1451 1-4 EEL = 531.1492 VDWAALS = 1412.1560 - EELEC = -12325.9779 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12325.9779 EHBOND = 0.0000 RESTRAINT = 0.0677 + EAMBER (non-restraint) = -10184.3397 Ewald error estimate: 0.7106E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.068 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.08 PRESS = 0.0 - Etot = -8316.3315 EKtot = 1897.7563 EPtot = -10214.0878 + Etot = -8316.2539 EKtot = 1897.7563 EPtot = -10214.0102 BOND = 27.6188 ANGLE = 63.5221 DIHED = 74.6915 1-4 NB = 34.5529 1-4 EEL = 531.0483 VDWAALS = 1411.0406 - EELEC = -12356.5621 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12356.5621 EHBOND = 0.0000 RESTRAINT = 0.0776 + EAMBER (non-restraint) = -10214.0878 Ewald error estimate: 0.2671E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.078 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 298.95 PRESS = 0.0 - Etot = -8320.6927 EKtot = 1890.6088 EPtot = -10211.3015 + Etot = -8320.6051 EKtot = 1890.6088 EPtot = -10211.2139 BOND = 29.0760 ANGLE = 59.1551 DIHED = 74.5904 1-4 NB = 35.5675 1-4 EEL = 533.2251 VDWAALS = 1407.8828 - EELEC = -12350.7985 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12350.7985 EHBOND = 0.0000 RESTRAINT = 0.0875 + EAMBER (non-restraint) = -10211.3015 Ewald error estimate: 0.1563E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.088 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.28 PRESS = 0.0 - Etot = -8323.4554 EKtot = 1930.6592 EPtot = -10254.1146 + Etot = -8323.3578 EKtot = 1930.6592 EPtot = -10254.0170 BOND = 22.6404 ANGLE = 69.8171 DIHED = 71.6234 1-4 NB = 35.1260 1-4 EEL = 535.0158 VDWAALS = 1393.3915 - EELEC = -12381.7288 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12381.7288 EHBOND = 0.0000 RESTRAINT = 0.0976 + EAMBER (non-restraint) = -10254.1146 Ewald error estimate: 0.1030E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.098 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.22 PRESS = 0.0 - Etot = -8317.7406 EKtot = 1904.9890 EPtot = -10222.7296 + Etot = -8317.6878 EKtot = 1904.9890 EPtot = -10222.6768 BOND = 27.4300 ANGLE = 66.6361 DIHED = 73.7311 1-4 NB = 32.0319 1-4 EEL = 535.7941 VDWAALS = 1380.9533 - EELEC = -12339.3061 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12339.3061 EHBOND = 0.0000 RESTRAINT = 0.0528 + EAMBER (non-restraint) = -10222.7296 Ewald error estimate: 0.1394E-03 ------------------------------------------------------------------------------ @@ -353,10 +407,11 @@ NGLY NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.48 PRESS = 0.0 - Etot = 6.0752 EKtot = 22.0042 EPtot = 23.1025 + Etot = 6.0806 EKtot = 22.0042 EPtot = 23.1033 BOND = 4.8942 ANGLE = 3.6306 DIHED = 1.2405 1-4 NB = 2.5044 1-4 EEL = 3.5318 VDWAALS = 38.2838 - EELEC = 40.2090 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 40.2090 EHBOND = 0.0000 RESTRAINT = 0.0286 + EAMBER (non-restraint) = 23.0747 Ewald error estimate: 0.1632E-03 ------------------------------------------------------------------------------ @@ -364,66 +419,77 @@ NGLY 5. TIMINGS -------------------------------------------------------------------------------- -| NonSetup CPU Time in Major Routines: +| NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ -| Nonbond 1.30 91.09 +| DataDistrib 0.01 2.34 +| Nonbond 0.20 81.26 | Bond 0.00 0.00 -| Angle 0.00 0.14 -| Dihedral 0.02 1.26 -| Shake 0.02 1.54 -| RunMD 0.08 5.82 -| Other 0.00 0.14 +| Angle 0.00 0.00 +| Dihedral 0.00 1.12 +| Shake 0.00 0.71 +| RunMD 0.03 14.26 +| Other 0.00 0.31 | ------------------------------ -| Total 1.43 +| Total 0.25 -| PME Nonbond Pairlist CPU Time: +| PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.00 -| Build List 0.23 16.20 +| Set Up Cit 0.00 0.20 +| Build List 0.02 8.04 | --------------------------------- -| Total 0.23 16.20 +| Total 0.02 8.25 -| PME Direct Force CPU Time: +| PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.72 50.49 -| Exclude Masked 0.01 0.63 -| Other 0.01 0.70 +| NonBonded Calc 0.12 46.95 +| Exclude Masked 0.00 1.32 +| Other 0.00 1.12 | --------------------------------- -| Total 0.74 51.82 +| Total 0.12 49.39 -| PME Reciprocal Force CPU Time: +| PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.02 1.54 -| Grid Charges 0.03 2.24 -| Scalar Sum 0.06 4.14 -| Gradient Sum 0.03 2.38 -| FFT 0.18 12.76 +| 1D bspline 0.01 2.24 +| Grid Charges 0.01 2.34 +| Scalar Sum 0.01 3.77 +| Gradient Sum 0.01 2.34 +| FFT 0.03 12.83 | --------------------------------- -| Total 0.33 23.07 +| Total 0.06 23.52 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.10 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.10 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 1.28 Per Step(ms) = 28.45 -| ns/day = 6.07 seconds/ns = 14226.57 +| Elapsed(s) = 0.22 Per Step(ms) = 4.86 +| ns/day = 35.57 seconds/ns = 2428.80 | | Average timings for all steps: -| Elapsed(s) = 1.43 Per Step(ms) = 28.52 -| ns/day = 6.06 seconds/ns = 14260.80 +| Elapsed(s) = 0.25 Per Step(ms) = 4.94 +| ns/day = 34.96 seconds/ns = 2471.19 | ----------------------------------------------------- -| Setup CPU time: 0.07 seconds -| NonSetup CPU time: 1.43 seconds -| Total CPU time: 1.50 seconds 0.00 hours +| Master Setup CPU time: 0.05 seconds +| Master NonSetup CPU time: 0.25 seconds +| Master Total CPU time: 0.30 seconds 0.00 hours -| Setup wall time: 0 seconds -| NonSetup wall time: 1 seconds -| Total wall time: 1 seconds 0.00 hours +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 0 seconds +| Master Total wall time: 0 seconds 0.00 hours diff --git test/nfe/abmd_FLOODING/save.sander/mdout test/nfe/abmd_FLOODING/save.sander/mdout index aed309ee58..023e8f11b8 100644 --- test/nfe/abmd_FLOODING/save.sander/mdout +++ test/nfe/abmd_FLOODING/save.sander/mdout @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/17/2016 at 18:29:37 +| Run on 09/01/2018 at 14:18:39 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/abmd_FLOODING -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abmd_FLOODING +| Hostname: gaia.physics.ncsu.edu File Assignments: @@ -45,7 +45,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -90,10 +90,10 @@ File Assignments: | Real 304361 | Hollerith 10444 | Integer 115557 -| Max Pairs 523832 +| Max Pairs 261916 | nblistReal 37716 -| nblist Int 108331 -| Total 5634 kbytes +| nblist Int 105664 +| Total 4600 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -164,11 +164,12 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 785 1571 2357 3143 +| 0 392 785 1178 1568 1961 2354 2744 +| 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 4 nodes +| Running AMBER/MPI version on 8 nodes -------------------------------------------------------------------------------- @@ -247,107 +248,148 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 164631 +| Local SIZE OF NONBOND LIST = 84063 | TOTAL SIZE OF NONBOND LIST = 650668 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.4834 EKtot = 1914.1823 EPtot = -10235.6657 + Etot = -8321.4754 EKtot = 1914.1823 EPtot = -10235.6577 BOND = 19.0733 ANGLE = 63.5926 DIHED = 72.6962 1-4 NB = 31.9325 1-4 EEL = 541.0002 VDWAALS = 1297.2732 - EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10235.6657 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.15 PRESS = 0.0 - Etot = -8329.3307 EKtot = 1917.1634 EPtot = -10246.4941 + Etot = -8329.3128 EKtot = 1917.1634 EPtot = -10246.4762 BOND = 25.2746 ANGLE = 68.1064 DIHED = 73.1044 1-4 NB = 34.0179 1-4 EEL = 541.6437 VDWAALS = 1326.2609 - EELEC = -12314.9020 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9020 EHBOND = 0.0000 RESTRAINT = 0.0179 + EAMBER (non-restraint) = -10246.4941 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 - Etot = -8320.0759 EKtot = 1879.6557 EPtot = -10199.7316 + Etot = -8320.0480 EKtot = 1879.6557 EPtot = -10199.7037 BOND = 25.7310 ANGLE = 67.7043 DIHED = 76.2867 1-4 NB = 31.4947 1-4 EEL = 535.0451 VDWAALS = 1359.5170 - EELEC = -12295.5104 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12295.5104 EHBOND = 0.0000 RESTRAINT = 0.0279 + EAMBER (non-restraint) = -10199.7316 Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.028 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 - Etot = -8311.9580 EKtot = 1892.0330 EPtot = -10203.9910 + Etot = -8311.9201 EKtot = 1892.0330 EPtot = -10203.9531 BOND = 32.8306 ANGLE = 68.2449 DIHED = 72.8985 1-4 NB = 28.3900 1-4 EEL = 536.4113 VDWAALS = 1387.0681 - EELEC = -12329.8344 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12329.8344 EHBOND = 0.0000 RESTRAINT = 0.0379 + EAMBER (non-restraint) = -10203.9910 Ewald error estimate: 0.2632E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.038 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.80 PRESS = 0.0 - Etot = -8313.5864 EKtot = 1908.6834 EPtot = -10222.2699 + Etot = -8313.5386 EKtot = 1908.6834 EPtot = -10222.2220 BOND = 35.4463 ANGLE = 70.8435 DIHED = 73.4767 1-4 NB = 28.8885 1-4 EEL = 538.8834 VDWAALS = 1406.8392 - EELEC = -12376.6474 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12376.6474 EHBOND = 0.0000 RESTRAINT = 0.0478 + EAMBER (non-restraint) = -10222.2699 Ewald error estimate: 0.3060E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.048 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.89 PRESS = 0.0 - Etot = -8308.1379 EKtot = 1947.1620 EPtot = -10255.2999 + Etot = -8308.0802 EKtot = 1947.1620 EPtot = -10255.2423 BOND = 32.8607 ANGLE = 64.4499 DIHED = 74.4288 1-4 NB = 30.2039 1-4 EEL = 534.5190 VDWAALS = 1408.1037 - EELEC = -12399.8659 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12399.8659 EHBOND = 0.0000 RESTRAINT = 0.0577 + EAMBER (non-restraint) = -10255.2999 Ewald error estimate: 0.7442E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.058 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 296.00 PRESS = 0.0 - Etot = -8312.3539 EKtot = 1871.9858 EPtot = -10184.3397 + Etot = -8312.2862 EKtot = 1871.9858 EPtot = -10184.2720 BOND = 23.7478 ANGLE = 70.9252 DIHED = 73.5149 1-4 NB = 30.1451 1-4 EEL = 531.1492 VDWAALS = 1412.1560 - EELEC = -12325.9779 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12325.9779 EHBOND = 0.0000 RESTRAINT = 0.0677 + EAMBER (non-restraint) = -10184.3397 Ewald error estimate: 0.7106E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.068 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.08 PRESS = 0.0 - Etot = -8316.3315 EKtot = 1897.7563 EPtot = -10214.0878 + Etot = -8316.2539 EKtot = 1897.7563 EPtot = -10214.0102 BOND = 27.6188 ANGLE = 63.5221 DIHED = 74.6915 1-4 NB = 34.5529 1-4 EEL = 531.0483 VDWAALS = 1411.0406 - EELEC = -12356.5621 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12356.5621 EHBOND = 0.0000 RESTRAINT = 0.0776 + EAMBER (non-restraint) = -10214.0878 Ewald error estimate: 0.2671E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.078 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 298.95 PRESS = 0.0 - Etot = -8320.6927 EKtot = 1890.6088 EPtot = -10211.3015 + Etot = -8320.6051 EKtot = 1890.6088 EPtot = -10211.2139 BOND = 29.0760 ANGLE = 59.1551 DIHED = 74.5904 1-4 NB = 35.5675 1-4 EEL = 533.2251 VDWAALS = 1407.8828 - EELEC = -12350.7985 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12350.7985 EHBOND = 0.0000 RESTRAINT = 0.0875 + EAMBER (non-restraint) = -10211.3015 Ewald error estimate: 0.1563E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.088 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.28 PRESS = 0.0 - Etot = -8323.4554 EKtot = 1930.6592 EPtot = -10254.1146 + Etot = -8323.3578 EKtot = 1930.6592 EPtot = -10254.0170 BOND = 22.6404 ANGLE = 69.8171 DIHED = 71.6234 1-4 NB = 35.1260 1-4 EEL = 535.0158 VDWAALS = 1393.3915 - EELEC = -12381.7288 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12381.7288 EHBOND = 0.0000 RESTRAINT = 0.0976 + EAMBER (non-restraint) = -10254.1146 Ewald error estimate: 0.1030E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.098 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 50 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 300.64 PRESS = 0.0 - Etot = -8317.3663 EKtot = 1901.3225 EPtot = -10218.6888 + Etot = -8317.3176 EKtot = 1901.3225 EPtot = -10218.6400 BOND = 28.9492 ANGLE = 67.5728 DIHED = 73.8193 1-4 NB = 31.9717 1-4 EEL = 536.0401 VDWAALS = 1376.2098 - EELEC = -12333.2516 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12333.2516 EHBOND = 0.0000 RESTRAINT = 0.0488 + EAMBER (non-restraint) = -10218.6888 Ewald error estimate: 0.1690E-03 ------------------------------------------------------------------------------ @@ -356,10 +398,11 @@ NGLY NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.25 PRESS = 0.0 - Etot = 6.9008 EKtot = 20.5587 EPtot = 20.6062 + Etot = 6.9132 EKtot = 20.5587 EPtot = 20.6109 BOND = 4.6086 ANGLE = 4.1032 DIHED = 1.9509 1-4 NB = 2.4045 1-4 EEL = 3.7524 VDWAALS = 43.5583 - EELEC = 42.1309 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 42.1309 EHBOND = 0.0000 RESTRAINT = 0.0287 + EAMBER (non-restraint) = 20.5822 Ewald error estimate: 0.1611E-03 ------------------------------------------------------------------------------ @@ -369,56 +412,57 @@ NGLY -------------------------------------------------------------------------------- |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> -| Read coords time 0.00 ( 0.27% of Total) +| Read coords time 0.00 ( 0.23% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.08 (72.51% of List ) -| Other 0.03 (27.49% of List ) -| List time 0.10 (12.95% of Nonbo) -| Short_ene time 0.46 (97.33% of Direc) -| Other 0.01 ( 2.67% of Direc) -| Direct Ewald time 0.47 (68.24% of Ewald) -| Adjust Ewald time 0.00 ( 0.53% of Ewald) +| Build the list 0.02 (63.03% of List ) +| Other 0.01 (36.97% of List ) +| List time 0.04 (15.62% of Nonbo) +| Short_ene time 0.13 (95.16% of Direc) +| Other 0.01 ( 4.84% of Direc) +| Direct Ewald time 0.14 (67.63% of Ewald) +| Adjust Ewald time 0.00 ( 0.45% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.01 ( 5.08% of Recip) -| Fill charge grid 0.01 ( 5.10% of Recip) -| Scalar sum 0.06 (27.60% of Recip) -| Grad sum 0.02 (10.98% of Recip) -| FFT back comm time 0.01 ( 6.33% of FFT t) -| Other 0.10 (93.67% of FFT t) -| FFT time 0.10 (50.93% of Recip) -| Other 0.00 ( 0.32% of Recip) -| Recip Ewald time 0.20 (29.14% of Ewald) -| Force Adjust 0.01 ( 1.76% of Ewald) -| Virial junk 0.00 ( 0.25% of Ewald) -| Other 0.00 ( 0.08% of Ewald) -| Ewald time 0.70 (87.05% of Nonbo) +| Fill Bspline coeffs 0.00 ( 9.20% of Recip) +| Fill charge grid 0.00 ( 6.41% of Recip) +| Scalar sum 0.01 (27.01% of Recip) +| Grad sum 0.01 (13.41% of Recip) +| FFT back comm time 0.00 (16.59% of FFT t) +| Other 0.02 (83.41% of FFT t) +| FFT time 0.02 (40.25% of Recip) +| Other 0.00 ( 3.72% of Recip) +| Recip Ewald time 0.05 (25.38% of Ewald) +| Force Adjust 0.01 ( 5.89% of Ewald) +| Virial junk 0.00 ( 0.54% of Ewald) +| Start synchronizatio 0.00 ( 0.01% of Ewald) +| Other 0.00 ( 0.09% of Ewald) +| Ewald time 0.20 (84.37% of Nonbo) | Other 0.00 ( 0.01% of Nonbo) -| Nonbond force 0.80 (96.08% of Force) -| Bond/Angle/Dihedral 0.00 ( 0.44% of Force) -| FRC Collect time 0.00 ( 0.38% of Force) -| Other 0.03 ( 3.10% of Force) -| Force time 0.83 (90.24% of Runmd) -| Shake time 0.00 ( 0.52% of Runmd) -| Verlet update time 0.08 ( 8.67% of Runmd) -| CRD distribute time 0.00 ( 0.17% of Runmd) -| Other 0.00 ( 0.41% of Runmd) -| Runmd Time 0.92 (93.10% of Total) -| Other 0.07 ( 6.61% of Total) -| Total time 0.99 (99.86% of ALL ) +| Nonbond force 0.24 (96.32% of Force) +| Bond/Angle/Dihedral 0.00 ( 0.42% of Force) +| FRC Collect time 0.00 ( 1.06% of Force) +| Other 0.01 ( 2.20% of Force) +| Force time 0.25 (82.08% of Runmd) +| Shake time 0.00 ( 0.41% of Runmd) +| Verlet update time 0.05 (15.76% of Runmd) +| CRD distribute time 0.00 ( 0.56% of Runmd) +| Other 0.00 ( 1.19% of Runmd) +| Runmd Time 0.30 (86.64% of Total) +| Other 0.05 (13.12% of Total) +| Total time 0.35 (99.70% of ALL ) | Number of list builds : 5 -| Highest rstack allocated: 72090 -| Highest istack allocated: 1396 +| Highest rstack allocated: 41935 +| Highest istack allocated: 931 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 0.92 Per Step(ms) = 18.48 -| ns/day = 9.35 seconds/ns = 9238.03 +| Elapsed(s) = 0.30 Per Step(ms) = 6.10 +| ns/day = 28.35 seconds/ns = 3048.07 | ----------------------------------------------------- -| Job began at 18:29:37.344 on 06/17/2016 -| Setup done at 18:29:37.415 on 06/17/2016 -| Run done at 18:29:38.338 on 06/17/2016 +| Job began at 14:18:39.298 on 09/01/2018 +| Setup done at 14:18:39.346 on 09/01/2018 +| Run done at 14:18:39.651 on 09/01/2018 | wallclock() was called 2783 times diff --git test/nfe/abmd_UMBRELLA/save.pmemd/mdout test/nfe/abmd_UMBRELLA/save.pmemd/mdout index d895118f1d..cabefb95fb 100644 --- test/nfe/abmd_UMBRELLA/save.pmemd/mdout +++ test/nfe/abmd_UMBRELLA/save.pmemd/mdout @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 06/03/2016 at 14:44:35 +| Run on 09/05/2018 at 13:07:47 -| Executable path: /home/feng/git_feng/amber/bin/pmemd -| Working directory: /home/feng/git_feng/amber/test/nfe/abmd_UMBRELLA -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abmd_UMBRELLA +| Hostname: gaia.physics.ncsu.edu File Assignments: | MDIN: mdin @@ -22,6 +22,7 @@ File Assignments: | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo +|LOGFILE: logfile | MDFRC: mdfrc @@ -34,7 +35,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -48,9 +49,11 @@ File Assignments: / +| irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: +| MPI | PUBFFT | BINTRAJ | EMIL @@ -140,6 +143,13 @@ Ewald parameters: Ewald Coefficient = 0.34864 Interpolation order = 4 +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- @@ -154,11 +164,14 @@ NGLY Forcing neutrality... | Dynamic Memory, Types Used: -| Reals 202260 -| Integers 79073 +| Reals 239932 +| Integers 206014 + +| Nonbonded Pairs Initial Allocation: 179151 -| Nonbonded Pairs Initial Allocation: 524959 +| Running AMBER/MPI version on 4 MPI task + -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- @@ -235,103 +248,144 @@ NGLY NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.4841 EKtot = 1914.1816 EPtot = -10235.6657 + Etot = -8321.3846 EKtot = 1914.1816 EPtot = -10235.5661 BOND = 19.0732 ANGLE = 63.5927 DIHED = 72.6962 1-4 NB = 31.9325 1-4 EEL = 541.0004 VDWAALS = 1297.2732 - EELEC = -12261.2339 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2339 EHBOND = 0.0000 RESTRAINT = 0.0995 + EAMBER (non-restraint) = -10235.6657 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.15 PRESS = 0.0 - Etot = -8329.3318 EKtot = 1917.1628 EPtot = -10246.4946 + Etot = -8329.2319 EKtot = 1917.1628 EPtot = -10246.3948 BOND = 25.2740 ANGLE = 68.1061 DIHED = 73.1045 1-4 NB = 34.0180 1-4 EEL = 541.6443 VDWAALS = 1326.2608 - EELEC = -12314.9024 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9024 EHBOND = 0.0000 RESTRAINT = 0.0999 + EAMBER (non-restraint) = -10246.4946 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 - Etot = -8320.0770 EKtot = 1879.6548 EPtot = -10199.7319 + Etot = -8319.9772 EKtot = 1879.6548 EPtot = -10199.6320 BOND = 25.7308 ANGLE = 67.7036 DIHED = 76.2868 1-4 NB = 31.4949 1-4 EEL = 535.0460 VDWAALS = 1359.5170 - EELEC = -12295.5110 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12295.5110 EHBOND = 0.0000 RESTRAINT = 0.0999 + EAMBER (non-restraint) = -10199.7319 Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 - Etot = -8311.9591 EKtot = 1892.0323 EPtot = -10203.9914 + Etot = -8311.8592 EKtot = 1892.0323 EPtot = -10203.8916 BOND = 32.8302 ANGLE = 68.2443 DIHED = 72.8985 1-4 NB = 28.3903 1-4 EEL = 536.4124 VDWAALS = 1387.0679 - EELEC = -12329.8351 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12329.8351 EHBOND = 0.0000 RESTRAINT = 0.0999 + EAMBER (non-restraint) = -10203.9914 Ewald error estimate: 0.2632E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.80 PRESS = 0.0 - Etot = -8313.5876 EKtot = 1908.6828 EPtot = -10222.2705 + Etot = -8313.4878 EKtot = 1908.6828 EPtot = -10222.1706 BOND = 35.4457 ANGLE = 70.8430 DIHED = 73.4767 1-4 NB = 28.8888 1-4 EEL = 538.8846 VDWAALS = 1406.8390 - EELEC = -12376.6483 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12376.6483 EHBOND = 0.0000 RESTRAINT = 0.0998 + EAMBER (non-restraint) = -10222.2705 Ewald error estimate: 0.3060E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.89 PRESS = 0.0 - Etot = -8308.1391 EKtot = 1947.1613 EPtot = -10255.3003 + Etot = -8308.0394 EKtot = 1947.1613 EPtot = -10255.2006 BOND = 32.8602 ANGLE = 64.4492 DIHED = 74.4288 1-4 NB = 30.2042 1-4 EEL = 534.5203 VDWAALS = 1408.1038 - EELEC = -12399.8669 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12399.8669 EHBOND = 0.0000 RESTRAINT = 0.0997 + EAMBER (non-restraint) = -10255.3003 Ewald error estimate: 0.7442E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 296.00 PRESS = 0.0 - Etot = -8312.3546 EKtot = 1871.9852 EPtot = -10184.3398 + Etot = -8312.2548 EKtot = 1871.9852 EPtot = -10184.2401 BOND = 23.7475 ANGLE = 70.9244 DIHED = 73.5149 1-4 NB = 30.1454 1-4 EEL = 531.1503 VDWAALS = 1412.1562 - EELEC = -12325.9785 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12325.9785 EHBOND = 0.0000 RESTRAINT = 0.0997 + EAMBER (non-restraint) = -10184.3398 Ewald error estimate: 0.7160E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.08 PRESS = 0.0 - Etot = -8316.3327 EKtot = 1897.7554 EPtot = -10214.0881 + Etot = -8316.2329 EKtot = 1897.7554 EPtot = -10213.9883 BOND = 27.6185 ANGLE = 63.5216 DIHED = 74.6915 1-4 NB = 34.5532 1-4 EEL = 531.0491 VDWAALS = 1411.0411 - EELEC = -12356.5630 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12356.5630 EHBOND = 0.0000 RESTRAINT = 0.0998 + EAMBER (non-restraint) = -10214.0881 Ewald error estimate: 0.2671E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 298.95 PRESS = 0.0 - Etot = -8320.6939 EKtot = 1890.6080 EPtot = -10211.3019 + Etot = -8320.5942 EKtot = 1890.6080 EPtot = -10211.2022 BOND = 29.0758 ANGLE = 59.1546 DIHED = 74.5904 1-4 NB = 35.5677 1-4 EEL = 533.2256 VDWAALS = 1407.8833 - EELEC = -12350.7994 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12350.7994 EHBOND = 0.0000 RESTRAINT = 0.0997 + EAMBER (non-restraint) = -10211.3019 Ewald error estimate: 0.1563E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.28 PRESS = 0.0 - Etot = -8323.4565 EKtot = 1930.6583 EPtot = -10254.1148 + Etot = -8323.3567 EKtot = 1930.6583 EPtot = -10254.0150 BOND = 22.6403 ANGLE = 69.8171 DIHED = 71.6235 1-4 NB = 35.1261 1-4 EEL = 535.0161 VDWAALS = 1393.3917 - EELEC = -12381.7295 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12381.7295 EHBOND = 0.0000 RESTRAINT = 0.0998 + EAMBER (non-restraint) = -10254.1148 Ewald error estimate: 0.1030E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.22 PRESS = 0.0 - Etot = -8317.7416 EKtot = 1904.9883 EPtot = -10222.7299 + Etot = -8317.6419 EKtot = 1904.9883 EPtot = -10222.6301 BOND = 27.4296 ANGLE = 66.6357 DIHED = 73.7312 1-4 NB = 32.0321 1-4 EEL = 535.7949 VDWAALS = 1380.9534 - EELEC = -12339.3068 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12339.3068 EHBOND = 0.0000 RESTRAINT = 0.0998 + EAMBER (non-restraint) = -10222.7299 Ewald error estimate: 0.1394E-03 ------------------------------------------------------------------------------ @@ -340,10 +394,11 @@ NGLY NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.48 PRESS = 0.0 - Etot = 6.0752 EKtot = 22.0042 EPtot = 23.1025 + Etot = 6.0752 EKtot = 22.0042 EPtot = 23.1026 BOND = 4.8941 ANGLE = 3.6306 DIHED = 1.2405 1-4 NB = 2.5043 1-4 EEL = 3.5317 VDWAALS = 38.2839 - EELEC = 40.2092 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 40.2092 EHBOND = 0.0000 RESTRAINT = 0.0001 + EAMBER (non-restraint) = 23.1025 Ewald error estimate: 0.1632E-03 ------------------------------------------------------------------------------ @@ -351,66 +406,77 @@ NGLY 5. TIMINGS -------------------------------------------------------------------------------- -| NonSetup CPU Time in Major Routines: +| NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ -| Nonbond 1.30 91.72 -| Bond 0.00 0.07 -| Angle 0.00 0.28 -| Dihedral 0.01 0.78 -| Shake 0.02 1.20 -| RunMD 0.08 5.80 -| Other 0.00 0.14 +| DataDistrib 0.01 2.95 +| Nonbond 0.20 81.28 +| Bond 0.00 0.10 +| Angle 0.00 0.00 +| Dihedral 0.00 0.51 +| Shake 0.00 0.92 +| RunMD 0.03 13.84 +| Other 0.00 0.41 | ------------------------------ -| Total 1.41 +| Total 0.25 -| PME Nonbond Pairlist CPU Time: +| PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.00 -| Build List 0.23 16.35 +| Set Up Cit 0.00 0.20 +| Build List 0.02 7.93 | --------------------------------- -| Total 0.23 16.35 +| Total 0.02 8.14 -| PME Direct Force CPU Time: +| PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.72 50.81 -| Exclude Masked 0.01 0.99 -| Other 0.01 0.50 +| NonBonded Calc 0.11 46.39 +| Exclude Masked 0.00 1.22 +| Other 0.00 1.63 | --------------------------------- -| Total 0.74 52.30 +| Total 0.12 49.24 -| PME Reciprocal Force CPU Time: +| PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.02 1.56 -| Grid Charges 0.03 2.12 -| Scalar Sum 0.06 4.46 -| Gradient Sum 0.04 3.18 -| FFT 0.17 11.75 +| 1D bspline 0.01 2.24 +| Grid Charges 0.01 2.24 +| Scalar Sum 0.01 3.97 +| Gradient Sum 0.01 3.66 +| FFT 0.03 11.70 | --------------------------------- -| Total 0.33 23.07 +| Total 0.06 23.81 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 1.27 Per Step(ms) = 28.19 -| ns/day = 6.13 seconds/ns = 14097.14 +| Elapsed(s) = 0.22 Per Step(ms) = 4.85 +| ns/day = 35.60 seconds/ns = 2427.30 | | Average timings for all steps: -| Elapsed(s) = 1.41 Per Step(ms) = 28.27 -| ns/day = 6.11 seconds/ns = 14136.10 +| Elapsed(s) = 0.25 Per Step(ms) = 4.94 +| ns/day = 34.96 seconds/ns = 2471.37 | ----------------------------------------------------- -| Setup CPU time: 0.07 seconds -| NonSetup CPU time: 1.41 seconds -| Total CPU time: 1.49 seconds 0.00 hours +| Master Setup CPU time: 0.05 seconds +| Master NonSetup CPU time: 0.25 seconds +| Master Total CPU time: 0.30 seconds 0.00 hours -| Setup wall time: 0 seconds -| NonSetup wall time: 1 seconds -| Total wall time: 1 seconds 0.00 hours +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 0 seconds +| Master Total wall time: 0 seconds 0.00 hours diff --git test/nfe/abmd_UMBRELLA/save.sander/mdout test/nfe/abmd_UMBRELLA/save.sander/mdout index 928a1c4861..8b071ec7e6 100644 --- test/nfe/abmd_UMBRELLA/save.sander/mdout +++ test/nfe/abmd_UMBRELLA/save.sander/mdout @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/17/2016 at 18:29:38 +| Run on 09/01/2018 at 14:27:56 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/abmd_UMBRELLA -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abmd_UMBRELLA +| Hostname: gaia.physics.ncsu.edu File Assignments: @@ -45,7 +45,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -83,10 +83,10 @@ File Assignments: | Real 304361 | Hollerith 10444 | Integer 115557 -| Max Pairs 523832 +| Max Pairs 261916 | nblistReal 37716 -| nblist Int 108331 -| Total 5634 kbytes +| nblist Int 105664 +| Total 4600 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -157,11 +157,12 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 785 1571 2357 3143 +| 0 392 785 1178 1568 1961 2354 2744 +| 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 4 nodes +| Running AMBER/MPI version on 8 nodes -------------------------------------------------------------------------------- @@ -234,107 +235,148 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 164631 +| Local SIZE OF NONBOND LIST = 84063 | TOTAL SIZE OF NONBOND LIST = 650668 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.4841 EKtot = 1914.1816 EPtot = -10235.6657 + Etot = -8321.3846 EKtot = 1914.1816 EPtot = -10235.5661 BOND = 19.0732 ANGLE = 63.5927 DIHED = 72.6962 1-4 NB = 31.9325 1-4 EEL = 541.0004 VDWAALS = 1297.2732 - EELEC = -12261.2339 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2339 EHBOND = 0.0000 RESTRAINT = 0.0995 + EAMBER (non-restraint) = -10235.6657 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.15 PRESS = 0.0 - Etot = -8329.3318 EKtot = 1917.1628 EPtot = -10246.4946 + Etot = -8329.2319 EKtot = 1917.1628 EPtot = -10246.3948 BOND = 25.2740 ANGLE = 68.1061 DIHED = 73.1045 1-4 NB = 34.0180 1-4 EEL = 541.6443 VDWAALS = 1326.2608 - EELEC = -12314.9024 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9024 EHBOND = 0.0000 RESTRAINT = 0.0999 + EAMBER (non-restraint) = -10246.4946 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 - Etot = -8320.0770 EKtot = 1879.6548 EPtot = -10199.7319 + Etot = -8319.9772 EKtot = 1879.6548 EPtot = -10199.6320 BOND = 25.7308 ANGLE = 67.7036 DIHED = 76.2868 1-4 NB = 31.4949 1-4 EEL = 535.0460 VDWAALS = 1359.5170 - EELEC = -12295.5110 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12295.5110 EHBOND = 0.0000 RESTRAINT = 0.0999 + EAMBER (non-restraint) = -10199.7319 Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 - Etot = -8311.9591 EKtot = 1892.0323 EPtot = -10203.9914 + Etot = -8311.8592 EKtot = 1892.0323 EPtot = -10203.8916 BOND = 32.8302 ANGLE = 68.2443 DIHED = 72.8985 1-4 NB = 28.3903 1-4 EEL = 536.4124 VDWAALS = 1387.0679 - EELEC = -12329.8351 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12329.8351 EHBOND = 0.0000 RESTRAINT = 0.0999 + EAMBER (non-restraint) = -10203.9914 Ewald error estimate: 0.2632E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.80 PRESS = 0.0 - Etot = -8313.5876 EKtot = 1908.6828 EPtot = -10222.2705 + Etot = -8313.4878 EKtot = 1908.6828 EPtot = -10222.1706 BOND = 35.4457 ANGLE = 70.8430 DIHED = 73.4767 1-4 NB = 28.8888 1-4 EEL = 538.8846 VDWAALS = 1406.8390 - EELEC = -12376.6483 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12376.6483 EHBOND = 0.0000 RESTRAINT = 0.0998 + EAMBER (non-restraint) = -10222.2705 Ewald error estimate: 0.3060E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.89 PRESS = 0.0 - Etot = -8308.1391 EKtot = 1947.1613 EPtot = -10255.3003 + Etot = -8308.0394 EKtot = 1947.1613 EPtot = -10255.2006 BOND = 32.8602 ANGLE = 64.4492 DIHED = 74.4288 1-4 NB = 30.2042 1-4 EEL = 534.5203 VDWAALS = 1408.1038 - EELEC = -12399.8669 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12399.8669 EHBOND = 0.0000 RESTRAINT = 0.0997 + EAMBER (non-restraint) = -10255.3003 Ewald error estimate: 0.7442E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 296.00 PRESS = 0.0 - Etot = -8312.3546 EKtot = 1871.9852 EPtot = -10184.3398 + Etot = -8312.2548 EKtot = 1871.9852 EPtot = -10184.2401 BOND = 23.7475 ANGLE = 70.9244 DIHED = 73.5149 1-4 NB = 30.1454 1-4 EEL = 531.1503 VDWAALS = 1412.1562 - EELEC = -12325.9785 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12325.9785 EHBOND = 0.0000 RESTRAINT = 0.0997 + EAMBER (non-restraint) = -10184.3398 Ewald error estimate: 0.7160E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.08 PRESS = 0.0 - Etot = -8316.3327 EKtot = 1897.7554 EPtot = -10214.0881 + Etot = -8316.2329 EKtot = 1897.7554 EPtot = -10213.9883 BOND = 27.6185 ANGLE = 63.5216 DIHED = 74.6915 1-4 NB = 34.5532 1-4 EEL = 531.0491 VDWAALS = 1411.0411 - EELEC = -12356.5630 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12356.5630 EHBOND = 0.0000 RESTRAINT = 0.0998 + EAMBER (non-restraint) = -10214.0881 Ewald error estimate: 0.2671E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 298.95 PRESS = 0.0 - Etot = -8320.6939 EKtot = 1890.6080 EPtot = -10211.3019 + Etot = -8320.5942 EKtot = 1890.6080 EPtot = -10211.2022 BOND = 29.0758 ANGLE = 59.1546 DIHED = 74.5904 1-4 NB = 35.5677 1-4 EEL = 533.2256 VDWAALS = 1407.8833 - EELEC = -12350.7994 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12350.7994 EHBOND = 0.0000 RESTRAINT = 0.0997 + EAMBER (non-restraint) = -10211.3019 Ewald error estimate: 0.1563E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.28 PRESS = 0.0 - Etot = -8323.4565 EKtot = 1930.6583 EPtot = -10254.1148 + Etot = -8323.3567 EKtot = 1930.6583 EPtot = -10254.0150 BOND = 22.6403 ANGLE = 69.8171 DIHED = 71.6235 1-4 NB = 35.1261 1-4 EEL = 535.0161 VDWAALS = 1393.3917 - EELEC = -12381.7295 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12381.7295 EHBOND = 0.0000 RESTRAINT = 0.0998 + EAMBER (non-restraint) = -10254.1148 Ewald error estimate: 0.1030E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.100 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 50 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 300.64 PRESS = 0.0 - Etot = -8317.3674 EKtot = 1901.3218 EPtot = -10218.6892 + Etot = -8317.2677 EKtot = 1901.3218 EPtot = -10218.5894 BOND = 28.9488 ANGLE = 67.5723 DIHED = 73.8193 1-4 NB = 31.9719 1-4 EEL = 536.0409 VDWAALS = 1376.2098 - EELEC = -12333.2523 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12333.2523 EHBOND = 0.0000 RESTRAINT = 0.0997 + EAMBER (non-restraint) = -10218.6892 Ewald error estimate: 0.1691E-03 ------------------------------------------------------------------------------ @@ -343,10 +385,11 @@ NGLY NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.25 PRESS = 0.0 - Etot = 6.9007 EKtot = 20.5587 EPtot = 20.6062 + Etot = 6.9008 EKtot = 20.5587 EPtot = 20.6062 BOND = 4.6086 ANGLE = 4.1032 DIHED = 1.9509 1-4 NB = 2.4044 1-4 EEL = 3.7522 VDWAALS = 43.5583 - EELEC = 42.1311 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 42.1311 EHBOND = 0.0000 RESTRAINT = 0.0002 + EAMBER (non-restraint) = 20.6061 Ewald error estimate: 0.1611E-03 ------------------------------------------------------------------------------ @@ -356,56 +399,56 @@ NGLY -------------------------------------------------------------------------------- |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> -| Read coords time 0.00 ( 0.29% of Total) +| Read coords time 0.00 ( 0.23% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.08 (72.68% of List ) -| Other 0.03 (27.32% of List ) -| List time 0.10 (13.75% of Nonbo) -| Short_ene time 0.47 (97.32% of Direc) -| Other 0.01 ( 2.68% of Direc) -| Direct Ewald time 0.48 (73.34% of Ewald) -| Adjust Ewald time 0.00 ( 0.57% of Ewald) +| Build the list 0.03 (65.11% of List ) +| Other 0.01 (34.89% of List ) +| List time 0.04 (16.35% of Nonbo) +| Short_ene time 0.13 (95.11% of Direc) +| Other 0.01 ( 4.89% of Direc) +| Direct Ewald time 0.14 (68.46% of Ewald) +| Adjust Ewald time 0.00 ( 0.46% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.01 ( 6.92% of Recip) -| Fill charge grid 0.01 ( 6.96% of Recip) -| Scalar sum 0.06 (37.36% of Recip) -| Grad sum 0.02 (14.95% of Recip) -| FFT back comm time 0.01 (12.58% of FFT t) -| Other 0.04 (87.42% of FFT t) -| FFT time 0.05 (33.36% of Recip) -| Other 0.00 ( 0.45% of Recip) -| Recip Ewald time 0.15 (22.90% of Ewald) -| Force Adjust 0.02 ( 2.85% of Ewald) -| Virial junk 0.00 ( 0.25% of Ewald) -| Other 0.00 ( 0.08% of Ewald) -| Ewald time 0.65 (86.25% of Nonbo) +| Fill Bspline coeffs 0.00 ( 9.33% of Recip) +| Fill charge grid 0.00 ( 6.35% of Recip) +| Scalar sum 0.01 (26.74% of Recip) +| Grad sum 0.01 (13.35% of Recip) +| FFT back comm time 0.00 (15.72% of FFT t) +| Other 0.02 (84.28% of FFT t) +| FFT time 0.02 (40.31% of Recip) +| Other 0.00 ( 3.92% of Recip) +| Recip Ewald time 0.05 (25.87% of Ewald) +| Force Adjust 0.01 ( 4.56% of Ewald) +| Virial junk 0.00 ( 0.54% of Ewald) +| Other 0.00 ( 0.10% of Ewald) +| Ewald time 0.20 (83.63% of Nonbo) | Other 0.00 ( 0.01% of Nonbo) -| Nonbond force 0.76 (98.05% of Force) -| Bond/Angle/Dihedral 0.00 ( 0.47% of Force) -| FRC Collect time 0.00 ( 0.41% of Force) -| Other 0.01 ( 1.07% of Force) -| Force time 0.77 (89.68% of Runmd) -| Shake time 0.00 ( 0.56% of Runmd) -| Verlet update time 0.08 ( 9.09% of Runmd) -| CRD distribute time 0.00 ( 0.18% of Runmd) -| Other 0.00 ( 0.49% of Runmd) -| Runmd Time 0.86 (92.70% of Total) -| Other 0.06 ( 7.00% of Total) -| Total time 0.93 (99.85% of ALL ) +| Nonbond force 0.24 (96.40% of Force) +| Bond/Angle/Dihedral 0.00 ( 0.42% of Force) +| FRC Collect time 0.00 ( 0.97% of Force) +| Other 0.01 ( 2.21% of Force) +| Force time 0.25 (82.77% of Runmd) +| Shake time 0.00 ( 0.41% of Runmd) +| Verlet update time 0.05 (15.41% of Runmd) +| CRD distribute time 0.00 ( 0.49% of Runmd) +| Other 0.00 ( 0.92% of Runmd) +| Runmd Time 0.30 (88.44% of Total) +| Other 0.04 (11.32% of Total) +| Total time 0.34 (99.72% of ALL ) | Number of list builds : 5 -| Highest rstack allocated: 72090 -| Highest istack allocated: 1396 +| Highest rstack allocated: 41935 +| Highest istack allocated: 931 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 0.86 Per Step(ms) = 17.24 -| ns/day = 10.02 seconds/ns = 8622.33 +| Elapsed(s) = 0.30 Per Step(ms) = 6.04 +| ns/day = 28.62 seconds/ns = 3018.78 | ----------------------------------------------------- -| Job began at 18:29:38.663 on 06/17/2016 -| Setup done at 18:29:38.733 on 06/17/2016 -| Run done at 18:29:39.595 on 06/17/2016 +| Job began at 14:27:56.354 on 09/01/2018 +| Setup done at 14:27:56.395 on 09/01/2018 +| Run done at 14:27:56.697 on 09/01/2018 | wallclock() was called 2783 times diff --git test/nfe/abremd/inpcrd.1 test/nfe/abremd/inpcrd.1 index 73d7aa7338..0289652b43 100644 --- test/nfe/abremd/inpcrd.1 +++ test/nfe/abremd/inpcrd.1 @@ -1,5 +1,5 @@ NGLY - 3143 0.0000000E+00 0.3200000E+03 + 3143 0.0000000E+00 -5.9099758 16.7611687 9.6964744 -6.6876601 16.2962589 10.1427587 -5.6077881 16.2415689 8.8848103 -6.0729168 17.6175205 9.1863747 -4.7182170 16.6491281 10.4618789 -4.3645304 15.6209508 10.3853468 diff --git test/nfe/abremd/inpcrd.2 test/nfe/abremd/inpcrd.2 index 2ee93e4c83..88fc07ea29 100644 --- test/nfe/abremd/inpcrd.2 +++ test/nfe/abremd/inpcrd.2 @@ -1,5 +1,5 @@ NGLY - 3143 0.0000000E+00 0.3000000E+03 + 3143 0.0000000E+00 -6.3647119 7.2118689 4.2338885 -5.7620774 6.8676748 3.5000899 -5.6693358 7.4541444 4.9251589 -6.7424291 8.0670351 3.8516314 -7.3862977 6.2756135 4.6925230 -8.1140353 6.0876054 3.9031273 diff --git test/nfe/abremd/inpcrd.3 test/nfe/abremd/inpcrd.3 index 3370f6a0c0..d5c10b2b42 100644 --- test/nfe/abremd/inpcrd.3 +++ test/nfe/abremd/inpcrd.3 @@ -1,5 +1,5 @@ NGLY - 3143 0.0000000E+00 0.3300000E+03 + 3143 0.0000000E+00 -4.8563545 15.0635235 25.8712062 -4.5271096 16.0127985 25.7683623 -3.9707341 14.5801650 25.9174805 -5.4031234 14.8420339 26.6910147 -5.6050883 14.7641396 24.6600085 -6.1061885 13.7996469 24.7421811 diff --git test/nfe/abremd/inpcrd.4 test/nfe/abremd/inpcrd.4 index fdc15b3027..4800fa9afd 100644 --- test/nfe/abremd/inpcrd.4 +++ test/nfe/abremd/inpcrd.4 @@ -1,5 +1,5 @@ NGLY - 3143 0.0000000E+00 0.3100000E+03 + 3143 0.0000000E+00 1.8785779 25.3661554 7.7188732 1.7220016 25.2727944 8.7122864 2.5527229 24.6529067 7.4803257 1.0934459 25.1537287 7.1200889 2.4401376 26.6274332 7.3917997 2.4565905 26.7008661 6.3044000 diff --git test/nfe/abremd/mdin.1 test/nfe/abremd/mdin.1 index ae84f5b258..64c1c3f298 100644 --- test/nfe/abremd/mdin.1 +++ test/nfe/abremd/mdin.1 @@ -4,7 +4,7 @@ ntb = 1, ntp = 0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, numexchg = 10 / diff --git test/nfe/abremd/mdin.2 test/nfe/abremd/mdin.2 index f0b759d13f..c7275b3721 100644 --- test/nfe/abremd/mdin.2 +++ test/nfe/abremd/mdin.2 @@ -4,7 +4,7 @@ ntb = 1, ntp = 0, temp0 = 310.0, ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, numexchg = 10 / diff --git test/nfe/abremd/mdin.3 test/nfe/abremd/mdin.3 index b0bf3a4e80..4aa871422c 100644 --- test/nfe/abremd/mdin.3 +++ test/nfe/abremd/mdin.3 @@ -4,7 +4,7 @@ ntb = 1, ntp = 0, temp0 = 320.0, ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, numexchg = 10 / diff --git test/nfe/abremd/mdin.4 test/nfe/abremd/mdin.4 index bbd678e6ff..e482ed1124 100644 --- test/nfe/abremd/mdin.4 +++ test/nfe/abremd/mdin.4 @@ -4,7 +4,7 @@ ntb = 1, ntp = 0, temp0 = 330.0, ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, numexchg = 10 / diff --git test/nfe/abremd/run-pmemd.sh test/nfe/abremd/run-pmemd.sh new file mode 100755 index 0000000000..25f119f488 --- /dev/null +++ test/nfe/abremd/run-pmemd.sh @@ -0,0 +1,65 @@ +#!/bin/sh +#TEST-PROGRAM sander +#TEST-DESCRIP TO_BE_DEtermined +#TEST-PURPOSE regression, basic +#TEST-STATE undocumented + +. ../common.sh + +# +# don't run if there is no netCDF +# + +set_NC_UTILS + +if test $? -ne 0; then + exit 0; +fi + +set_SANDER pmemd.MPI +set_SANDER_CMD 4 + +JUNK="umbrella.?.nc mdout.? restrt.? abmd.?.txt logfile.*" +JUNK="${JUNK} mdcrd.? groups prmtop sander.out *.log *.type *.ncdump" + +# +# remove the junk +# + +/bin/rm -rf ${JUNK} junk.* + +# +# prepare files +# + +cp -p ../prmtop ../groups . + +# +# run SANDER +# + +${SANDER_CMD} -ng 4 -rem 3 -groupfile groups > sander.out 2>&1 + +../../dacdif save.pmemd/rem.log rem.log + +for i in 1 2 3 4; do + ../../dacdif -t 1 save.pmemd/abmd.$i.txt abmd.$i.txt + ../../dacdif -t 1 save.pmemd/mdout.$i mdout.$i +done + +for i in 1 2 3 4; do + do_ncdump '%14.10f' umbrella.$i.nc umbrella.$i.ncdump + ../../dacdif save.pmemd/umbrella.$i.ncdump umbrella.$i.ncdump +done + +# +# preserve the junk on failure +# + +save_junk_on_failure ${JUNK} + +# +# remove the junk +# + +/bin/rm -f ${JUNK} profile_mpi diff --git test/nfe/abremd/run-sander.sh test/nfe/abremd/run-sander.sh index 78be75c238..0f0bf77bbe 100755 --- test/nfe/abremd/run-sander.sh +++ test/nfe/abremd/run-sander.sh @@ -20,7 +20,7 @@ set_SANDER sander.MPI set_SANDER_CMD 4 JUNK="umbrella.?.nc mdout.? restrt.? abmd.?.txt" -JUNK="${JUNK} mdcrd.? groups prmtop sander.out *.log *.type" +JUNK="${JUNK} mdcrd.? groups prmtop sander.out *.log *.type *.ncdump" # # remove the junk @@ -38,21 +38,18 @@ cp -p ../prmtop ../groups . # run SANDER # -${SANDER_CMD} -ng 4 -rem 1 -groupfile groups > sander.out 2>&1 +${SANDER_CMD} -ng 4 -rem 3 -groupfile groups > sander.out 2>&1 ../../dacdif save/rem.log rem.log -../../dacdif save/nfe-abmd.log nfe-abmd.log - for i in 1 2 3 4; do ../../dacdif -t 1 save/abmd.$i.txt abmd.$i.txt ../../dacdif -t 1 save/mdout.$i mdout.$i done for i in 1 2 3 4; do - do_ncdump '%14.10f' save/umbrella.$i.nc umbrella.$i.save.ncdump do_ncdump '%14.10f' umbrella.$i.nc umbrella.$i.ncdump - ../../dacdif umbrella.$i.save.ncdump umbrella.$i.ncdump + ../../dacdif save/umbrella.$i.ncdump umbrella.$i.ncdump done # @@ -65,4 +62,4 @@ save_junk_on_failure ${JUNK} # remove the junk # -/bin/rm -f ${JUNK} *.ncdump profile_mpi +/bin/rm -f ${JUNK} profile_mpi diff --git test/nfe/abremd/save.pmemd/abmd.1.txt test/nfe/abremd/save.pmemd/abmd.1.txt new file mode 100644 index 0000000000..3bbea0e02e --- /dev/null +++ test/nfe/abremd/save.pmemd/abmd.1.txt @@ -0,0 +1,53 @@ +# +# MD time (ps), CV #1, E_{bias} (kcal/mol) +# + 0.0000 6.5186874308 0.0000000000 + 0.0020 6.3050205790 0.0004959507 + 0.0040 6.3057900515 0.0024925729 + 0.0060 6.3062799104 0.0044870815 + 0.0080 6.3065657553 0.0064800871 + 0.0100 6.3065316739 0.0084708728 + 0.0120 7.3563766915 0.0000000000 + 0.0140 7.3544212824 0.0019970173 + 0.0160 7.3526015924 0.0039926818 + 0.0180 7.3508913389 0.0059868061 + 0.0200 7.3494821820 0.0079798500 + 0.0220 7.3482350958 0.0099718543 + 0.0240 7.3469045872 0.0119619421 + 0.0260 7.3455287926 0.0139498768 + 0.0280 7.3440827998 0.0159350978 + 0.0300 7.3423780778 0.0179153105 + 0.0320 7.3405832170 0.0198907311 + 0.0340 7.3386708872 0.0218600882 + 0.0360 7.3366354088 0.0238220851 + 0.0380 7.3345238741 0.0257762711 + 0.0400 7.3322711644 0.0277200447 + 0.0420 7.3298522500 0.0296508421 + 0.0440 7.3272134593 0.0315645515 + 0.0460 7.3243096514 0.0334560444 + 0.0480 7.3211135368 0.0353194903 + 0.0500 7.3175976130 0.0371477186 + 0.0520 6.2949459753 0.0103517767 + 0.0540 6.2937878866 0.0123296190 + 0.0560 6.2927427825 0.0143084882 + 0.0580 6.2914862531 0.0162839208 + 0.0600 6.2902006696 0.0182580129 + 0.0620 6.2888722500 0.0202302960 + 0.0640 6.2874302505 0.0221991993 + 0.0660 6.2858374739 0.0241633069 + 0.0680 6.2839606644 0.0261186716 + 0.0700 6.2820373450 0.0280687724 + 0.0720 6.2801283586 0.0300145015 + 0.0740 6.2785822971 0.0319659677 + 0.0760 6.2772032643 0.0339192891 + 0.0780 6.2761362567 0.0358802712 + 0.0800 6.2754672964 0.0378534753 + 0.0820 6.2750613699 0.0398354297 + 0.0840 6.2746965702 0.0418186850 + 0.0860 6.2744397773 0.0438057393 + 0.0880 6.2742466271 0.0457950856 + 0.0900 6.2742410679 0.0477913058 + 0.0920 7.2671663495 0.0342860349 + 0.0940 7.2659414349 0.0361121730 + 0.0960 7.2643857343 0.0378886595 + 0.0980 7.2627955272 0.0396561622 diff --git test/nfe/abremd/save.pmemd/abmd.2.txt test/nfe/abremd/save.pmemd/abmd.2.txt new file mode 100644 index 0000000000..4eeb74796a --- /dev/null +++ test/nfe/abremd/save.pmemd/abmd.2.txt @@ -0,0 +1,28 @@ +# +# MD time (ps), CV #1, E_{bias} (kcal/mol) +# + 0.0000 7.3651005026 0.0000000000 + 0.0040 7.3628045565 0.0019986832 + 0.0080 7.3600812668 0.0039953788 + 0.0120 6.3061196839 0.0000000000 + 0.0160 6.3048398753 0.0019910668 + 0.0200 6.3042719547 0.0039821857 + 0.0240 6.3049894012 0.0059732733 + 0.0280 6.3053948974 0.0079642424 + 0.0320 6.3043633733 0.0099555889 + 0.0360 6.3020981868 0.0119453924 + 0.0400 6.3000360590 0.0139328300 + 0.0440 6.2985558846 0.0159198033 + 0.0480 6.2969893049 0.0179048279 + 0.0520 7.3139804986 0.0055933661 + 0.0560 7.3064803197 0.0074596439 + 0.0600 7.2991693764 0.0093096278 + 0.0640 7.2931108721 0.0111666962 + 0.0680 7.2882026274 0.0130362228 + 0.0720 7.2833114996 0.0148923819 + 0.0760 7.2781451507 0.0167232844 + 0.0800 7.2733052557 0.0185459266 + 0.0840 7.2705137974 0.0204332427 + 0.0880 7.2690758324 0.0223712310 + 0.0920 6.2746970644 0.0195270296 + 0.0960 6.2769536642 0.0215841489 diff --git test/nfe/abremd/save.pmemd/abmd.3.txt test/nfe/abremd/save.pmemd/abmd.3.txt new file mode 100644 index 0000000000..43f6fe8c4f --- /dev/null +++ test/nfe/abremd/save.pmemd/abmd.3.txt @@ -0,0 +1,20 @@ +# +# MD time (ps), CV #1, E_{bias} (kcal/mol) +# + 0.0000 8.0143490198 0.0000000000 + 0.0060 8.0227202554 0.0014959505 + 0.0120 6.5220467082 0.0000000000 + 0.0180 6.5216703743 0.0014977429 + 0.0240 6.5228366017 0.0029950282 + 0.0300 6.5271381817 0.0044877117 + 0.0360 6.5332083905 0.0059680866 + 0.0420 6.5389200978 0.0074361520 + 0.0480 6.5453447457 0.0088829851 + 0.0540 8.0935872462 0.0030762400 + 0.0600 8.1016779940 0.0044833093 + 0.0660 8.1095564041 0.0058809450 + 0.0720 8.1125634859 0.0073370859 + 0.0780 8.1188580222 0.0087354393 + 0.0840 8.1281010114 0.0100506904 + 0.0900 8.1317986939 0.0114627228 + 0.0960 8.1309061097 0.0129844723 diff --git test/nfe/abremd/save.pmemd/abmd.4.txt test/nfe/abremd/save.pmemd/abmd.4.txt new file mode 100644 index 0000000000..b1e892b2a3 --- /dev/null +++ test/nfe/abremd/save.pmemd/abmd.4.txt @@ -0,0 +1,13 @@ +# +# MD time (ps), CV #1, E_{bias} (kcal/mol) +# + 0.0000 6.3043274285 0.0000000000 + 0.0100 6.5218632248 0.0083968696 + 0.0200 8.0462771334 0.0079510125 + 0.0300 8.0665380732 0.0176846389 + 0.0400 8.0820781744 0.0272155686 + 0.0500 8.0904626990 0.0368206435 + 0.0600 6.5633242869 0.0175999535 + 0.0700 6.5778903733 0.0270088561 + 0.0800 6.5880070039 0.0364371189 + 0.0900 6.5895472928 0.0463111070 diff --git test/nfe/abremd/save.pmemd/mdout.1 test/nfe/abremd/save.pmemd/mdout.1 new file mode 100644 index 0000000000..c78189fd5a --- /dev/null +++ test/nfe/abremd/save.pmemd/mdout.1 @@ -0,0 +1,445 @@ + + ------------------------------------------------------- + Amber 18 PMEMD 2018 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 18 + +| Run on 09/21/2018 at 19:22:17 + +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abremd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output + +File Assignments: +| MDIN: mdin.1 +| MDOUT: mdout.1 +| INPCRD: inpcrd.1 +| PARM: prmtop +| RESTRT: restrt.1 +| REFC: refc +| MDVEL: mdvel.000 +| MDEN: mden.000 +| MDCRD: mdcrd.1 +| MDINFO: /dev/null +|LOGFILE: logfile.000 +| MDFRC: mdfrc.000 + + + Here is the input file: + + + &cntrl + igb = 0, ntx = 7, irest = 1, + ntb = 1, ntp = 0, temp0 = 300.0, + ntt = 3, gamma_ln = 1.0, + ntf = 2, ntc = 2, tol = 0.00001, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, + numexchg = 10 + / + + &abmd + monitor_file = 'abmd.1.txt' + monitor_freq = 1 + + umbrella_file = 'umbrella.1.nc' + + mode = 'FLOODING' + + timescale = 1.0 + + cv_file = 'cv.in' + / + + +| irandom = 1, using AMBER's internal random number generator (default). + + +| Conditional Compilation Defines Used: +| MPI +| PUBFFT +| BINTRAJ +| EMIL + +| Largest sphere to fit in unit cell has radius = 14.075 + +| New format PARM file being parsed. +| Version = 1.000 Date = 09/01/07 Time = 11:29:05 + +| Note: 1-4 EEL scale factors were NOT found in the topology file. +| Using default value of 1.2. + +| Note: 1-4 VDW scale factors were NOT found in the topology file. +| Using default value of 2.0. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 + NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 + NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 + NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 + NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 + IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 6 6 6 +| Direct force subcell size = 5.7460 5.7460 5.7460 + + BOX TYPE: TRUNCATED OCTAHEDRON + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + +NGLY + +General flags: + imin = 0, nmropt = 0 + +Replica exchange + numexchg= 10, rem= 3 + +Nature and format of input: + ntx = 7, irest = 1, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 5, ntrx = 1, ntwr = 50 + iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 2, ntb = 1, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 0 + +Molecular dynamics: + nstlim = 5, nscm = 1000, nrespa = 1 + t = 0.00000, dt = 0.00200, vlimit = 20.00000 + +Langevin dynamics temperature regulation: + ig = 71277 + temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000 + +SHAKE: + ntc = 2, jfastw = 0 + tol = 0.00001 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 5 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 1 + Box X = 34.476 Box Y = 34.476 Box Z = 34.476 + Alpha = 109.471 Beta = 109.471 Gamma = 109.471 + NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + +NGLY + begin time read from input coords = 0.000 ps + + + Number of triangulated 3-point waters found: 1001 + + Sum of charges from parm topology file = -0.00000001 + Forcing neutrality... + +| Dynamic Memory, Types Used: +| Reals 245734 +| Integers 212431 + +| Nonbonded Pairs Initial Allocation: 358302 + +| Running AMBER/MPI version on 2 MPI task + + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + --------------------------------------------------- + APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION + using 5000.0 points per unit in tabled values + TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff +| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 +| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 + --------------------------------------------------- +|--------------------------------------------------- +| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.47 +| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.89 +|--------------------------------------------------- + + NFE : () () () () () () () () () () A. B. M. D. () () () () () () () () () + NFE : + NFE : mode = FLOODING + NFE : + NFE : CV #1 + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : monitor_file = abmd.1.txt + NFE : monitor_freq = 1 (0.0020 ps) + NFE : umbrella_file = umbrella.1.nc (not found) + NFE : + NFE : umbrella discretization (new) : + NFE : CV #1 not periodic, 97 points, min/max = 0.000000/12.000000 + NFE : + NFE : flooding timescale = 1.000 ps + NFE : + NFE : () () () () () () () () () () () () () () () () () () () () () () () () + + + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 281.56 PRESS = 0.0 + Etot = -8485.5418 EKtot = 1780.6314 EPtot = -10266.1732 + BOND = 28.3261 ANGLE = 51.6386 DIHED = 71.6224 + 1-4 NB = 28.8645 1-4 EEL = 540.6129 VDWAALS = 1437.6257 + EELEC = -12424.8699 EHBOND = 0.0000 RESTRAINT = 0.0065 + EAMBER (non-restraint) = -10266.1797 + Ewald error estimate: 0.4452E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.006 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 282.73 PRESS = 0.0 + Etot = -8500.5704 EKtot = 1788.0399 EPtot = -10288.6103 + BOND = 22.7739 ANGLE = 77.7414 DIHED = 75.2236 + 1-4 NB = 31.1806 1-4 EEL = 514.8200 VDWAALS = 1409.3457 + EELEC = -12419.7016 EHBOND = 0.0000 RESTRAINT = 0.0060 + EAMBER (non-restraint) = -10288.6163 + Ewald error estimate: 0.3772E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.006 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 281.87 PRESS = 0.0 + Etot = -8485.3639 EKtot = 1782.6102 EPtot = -10267.9740 + BOND = 25.6634 ANGLE = 68.9034 DIHED = 77.2181 + 1-4 NB = 32.3389 1-4 EEL = 518.7028 VDWAALS = 1411.9494 + EELEC = -12402.7660 EHBOND = 0.0000 RESTRAINT = 0.0159 + EAMBER (non-restraint) = -10267.9900 + Ewald error estimate: 0.3089E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.016 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 286.39 PRESS = 0.0 + Etot = -8477.4555 EKtot = 1811.1847 EPtot = -10288.6402 + BOND = 24.5019 ANGLE = 69.9706 DIHED = 70.7583 + 1-4 NB = 30.7480 1-4 EEL = 522.6107 VDWAALS = 1409.7292 + EELEC = -12416.9848 EHBOND = 0.0000 RESTRAINT = 0.0258 + EAMBER (non-restraint) = -10288.6660 + Ewald error estimate: 0.1417E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.026 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 285.48 PRESS = 0.0 + Etot = -8464.8690 EKtot = 1805.4274 EPtot = -10270.2964 + BOND = 25.8438 ANGLE = 68.4407 DIHED = 73.3978 + 1-4 NB = 34.4474 1-4 EEL = 526.8911 VDWAALS = 1420.2640 + EELEC = -12419.6164 EHBOND = 0.0000 RESTRAINT = 0.0353 + EAMBER (non-restraint) = -10270.3317 + Ewald error estimate: 0.2211E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.035 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 278.55 PRESS = 0.0 + Etot = -8473.9905 EKtot = 1761.6080 EPtot = -10235.5985 + BOND = 25.1293 ANGLE = 54.6139 DIHED = 75.2850 + 1-4 NB = 34.5101 1-4 EEL = 534.3233 VDWAALS = 1430.1674 + EELEC = -12389.6437 EHBOND = 0.0000 RESTRAINT = 0.0163 + EAMBER (non-restraint) = -10235.6148 + Ewald error estimate: 0.3339E-05 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.016 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 289.15 PRESS = 0.0 + Etot = -8466.5250 EKtot = 1828.6772 EPtot = -10295.2022 + BOND = 20.2902 ANGLE = 64.2051 DIHED = 79.4738 + 1-4 NB = 33.3934 1-4 EEL = 539.3367 VDWAALS = 1423.2999 + EELEC = -12455.2275 EHBOND = 0.0000 RESTRAINT = 0.0261 + EAMBER (non-restraint) = -10295.2283 + Ewald error estimate: 0.3757E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.026 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 278.90 PRESS = 0.0 + Etot = -8463.2639 EKtot = 1763.8512 EPtot = -10227.1151 + BOND = 28.5550 ANGLE = 53.2424 DIHED = 79.6043 + 1-4 NB = 33.0468 1-4 EEL = 541.5731 VDWAALS = 1425.2681 + EELEC = -12388.4407 EHBOND = 0.0000 RESTRAINT = 0.0359 + EAMBER (non-restraint) = -10227.1510 + Ewald error estimate: 0.2589E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.036 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 284.69 PRESS = 0.0 + Etot = -8471.3892 EKtot = 1800.4280 EPtot = -10271.8173 + BOND = 27.4332 ANGLE = 54.3325 DIHED = 76.5792 + 1-4 NB = 32.5746 1-4 EEL = 544.9752 VDWAALS = 1441.0374 + EELEC = -12448.7951 EHBOND = 0.0000 RESTRAINT = 0.0458 + EAMBER (non-restraint) = -10271.8630 + Ewald error estimate: 0.1330E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.046 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 284.04 PRESS = 0.0 + Etot = -8454.5768 EKtot = 1796.3375 EPtot = -10250.9143 + BOND = 27.8334 ANGLE = 67.3063 DIHED = 71.5455 + 1-4 NB = 32.7790 1-4 EEL = 518.9435 VDWAALS = 1384.4627 + EELEC = -12353.8244 EHBOND = 0.0000 RESTRAINT = 0.0397 + EAMBER (non-restraint) = -10250.9540 + Ewald error estimate: 0.1340E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.040 + BBMD : 0.000 STSM : 0.000 +=============================================================================== +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines, Average for All Tasks: +| +| Routine Sec % +| ------------------------------ +| DataDistrib 0.15 12.95 +| Nonbond 0.64 57.14 +| Bond 0.00 0.00 +| Angle 0.00 0.18 +| Dihedral 0.00 0.27 +| Shake 0.00 0.44 +| RunMD 0.26 22.72 +| Other 0.07 6.30 +| ------------------------------ +| Total 1.13 + +| PME Nonbond Pairlist CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.18 +| Build List 0.13 11.85 +| --------------------------------- +| Total 0.14 12.02 + +| PME Direct Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.33 29.28 +| Exclude Masked 0.01 0.58 +| Other 0.01 0.93 +| --------------------------------- +| Total 0.35 30.79 + +| PME Reciprocal Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.01 1.24 +| Grid Charges 0.01 0.93 +| Scalar Sum 0.03 2.48 +| Gradient Sum 0.01 0.93 +| FFT 0.10 8.74 +| --------------------------------- +| Total 0.16 14.33 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 + +| Final Performance Info: +| ----------------------------------------------------- +| Average timings for last 45 steps: +| Elapsed(s) = 0.99 Per Step(ms) = 22.08 +| ns/day = 7.83 seconds/ns = 11038.11 +| +| Average timings for all steps: +| Elapsed(s) = 1.13 Per Step(ms) = 22.60 +| ns/day = 7.64 seconds/ns = 11302.08 +| ----------------------------------------------------- + +| Master Setup CPU time: 0.06 seconds +| Master NonSetup CPU time: 1.13 seconds +| Master Total CPU time: 1.19 seconds 0.00 hours + +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds +| Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/abremd/save.pmemd/mdout.2 test/nfe/abremd/save.pmemd/mdout.2 new file mode 100644 index 0000000000..ddf17f9e62 --- /dev/null +++ test/nfe/abremd/save.pmemd/mdout.2 @@ -0,0 +1,445 @@ + + ------------------------------------------------------- + Amber 18 PMEMD 2018 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 18 + +| Run on 09/21/2018 at 19:22:17 + +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abremd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output + +File Assignments: +| MDIN: mdin.2 +| MDOUT: mdout.2 +| INPCRD: inpcrd.2 +| PARM: prmtop +| RESTRT: restrt.2 +| REFC: refc +| MDVEL: mdvel.001 +| MDEN: mden.001 +| MDCRD: mdcrd.2 +| MDINFO: /dev/null +|LOGFILE: logfile.001 +| MDFRC: mdfrc.001 + + + Here is the input file: + + + &cntrl + igb = 0, ntx = 7, irest = 1, + ntb = 1, ntp = 0, temp0 = 310.0, + ntt = 3, gamma_ln = 1.0, + ntf = 2, ntc = 2, tol = 0.00001, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, + numexchg = 10 + / + + &abmd + monitor_file = 'abmd.2.txt' + monitor_freq = 2 + + umbrella_file = 'umbrella.2.nc' + + mode = 'FLOODING' + + timescale = 2.0 + + cv_file = 'cv.in' + / + + +| irandom = 1, using AMBER's internal random number generator (default). + + +| Conditional Compilation Defines Used: +| MPI +| PUBFFT +| BINTRAJ +| EMIL + +| Largest sphere to fit in unit cell has radius = 14.075 + +| New format PARM file being parsed. +| Version = 1.000 Date = 09/01/07 Time = 11:29:05 + +| Note: 1-4 EEL scale factors were NOT found in the topology file. +| Using default value of 1.2. + +| Note: 1-4 VDW scale factors were NOT found in the topology file. +| Using default value of 2.0. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 + NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 + NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 + NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 + NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 + IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 6 6 6 +| Direct force subcell size = 5.7460 5.7460 5.7460 + + BOX TYPE: TRUNCATED OCTAHEDRON + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + +NGLY + +General flags: + imin = 0, nmropt = 0 + +Replica exchange + numexchg= 10, rem= 3 + +Nature and format of input: + ntx = 7, irest = 1, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 5, ntrx = 1, ntwr = 50 + iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 2, ntb = 1, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 0 + +Molecular dynamics: + nstlim = 5, nscm = 1000, nrespa = 1 + t = 0.00000, dt = 0.00200, vlimit = 20.00000 + +Langevin dynamics temperature regulation: + ig = 71277 + temp0 = 310.00000, tempi = 0.00000, gamma_ln= 1.00000 + +SHAKE: + ntc = 2, jfastw = 0 + tol = 0.00001 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 5 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 1 + Box X = 34.476 Box Y = 34.476 Box Z = 34.476 + Alpha = 109.471 Beta = 109.471 Gamma = 109.471 + NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + +NGLY + begin time read from input coords = 0.000 ps + + + Number of triangulated 3-point waters found: 1001 + + Sum of charges from parm topology file = -0.00000001 + Forcing neutrality... + +| Dynamic Memory, Types Used: +| Reals 245722 +| Integers 210813 + +| Nonbonded Pairs Initial Allocation: 358302 + +| Running AMBER/MPI version on 2 MPI task + + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + --------------------------------------------------- + APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION + using 5000.0 points per unit in tabled values + TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff +| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 +| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 + --------------------------------------------------- +|--------------------------------------------------- +| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.47 +| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.89 +|--------------------------------------------------- + + NFE : () () () () () () () () () () A. B. M. D. () () () () () () () () () + NFE : + NFE : mode = FLOODING + NFE : + NFE : CV #1 + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : monitor_file = abmd.2.txt + NFE : monitor_freq = 2 (0.0040 ps) + NFE : umbrella_file = umbrella.2.nc (not found) + NFE : + NFE : umbrella discretization (new) : + NFE : CV #1 not periodic, 97 points, min/max = 0.000000/12.000000 + NFE : + NFE : flooding timescale = 2.000 ps + NFE : + NFE : () () () () () () () () () () () () () () () () () () () () () () () () + + + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 296.01 PRESS = 0.0 + Etot = -8442.7202 EKtot = 1872.0385 EPtot = -10314.7587 + BOND = 28.7973 ANGLE = 68.1657 DIHED = 69.9843 + 1-4 NB = 30.9606 1-4 EEL = 509.2245 VDWAALS = 1396.6565 + EELEC = -12418.5516 EHBOND = 0.0000 RESTRAINT = 0.0040 + EAMBER (non-restraint) = -10314.7627 + Ewald error estimate: 0.4603E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.004 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 286.07 PRESS = 0.0 + Etot = -8428.4794 EKtot = 1809.1959 EPtot = -10237.6753 + BOND = 28.4848 ANGLE = 65.6220 DIHED = 84.4329 + 1-4 NB = 29.7197 1-4 EEL = 535.1655 VDWAALS = 1433.8230 + EELEC = -12414.9262 EHBOND = 0.0000 RESTRAINT = 0.0030 + EAMBER (non-restraint) = -10237.6782 + Ewald error estimate: 0.3550E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.003 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 280.35 PRESS = 0.0 + Etot = -8423.9018 EKtot = 1772.9960 EPtot = -10196.8978 + BOND = 30.2827 ANGLE = 61.6854 DIHED = 83.3316 + 1-4 NB = 28.8639 1-4 EEL = 528.6148 VDWAALS = 1444.2094 + EELEC = -12373.8936 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10196.9057 + Ewald error estimate: 0.2608E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 282.08 PRESS = 0.0 + Etot = -8410.5828 EKtot = 1783.9134 EPtot = -10194.4962 + BOND = 33.4399 ANGLE = 67.3820 DIHED = 78.0307 + 1-4 NB = 30.6470 1-4 EEL = 537.9277 VDWAALS = 1439.9106 + EELEC = -12381.8470 EHBOND = 0.0000 RESTRAINT = 0.0129 + EAMBER (non-restraint) = -10194.5092 + Ewald error estimate: 0.2484E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.013 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 288.73 PRESS = 0.0 + Etot = -8417.6130 EKtot = 1825.9965 EPtot = -10243.6095 + BOND = 24.3033 ANGLE = 56.7175 DIHED = 83.0985 + 1-4 NB = 32.6221 1-4 EEL = 537.5005 VDWAALS = 1438.1635 + EELEC = -12416.0329 EHBOND = 0.0000 RESTRAINT = 0.0179 + EAMBER (non-restraint) = -10243.6274 + Ewald error estimate: 0.7670E-04 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 290.19 PRESS = 0.0 + Etot = -8390.9630 EKtot = 1835.2411 EPtot = -10226.2042 + BOND = 20.1724 ANGLE = 75.7803 DIHED = 70.8407 + 1-4 NB = 32.2808 1-4 EEL = 524.3381 VDWAALS = 1436.4806 + EELEC = -12386.1055 EHBOND = 0.0000 RESTRAINT = 0.0084 + EAMBER (non-restraint) = -10226.2126 + Ewald error estimate: 0.1531E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 289.29 PRESS = 0.0 + Etot = -8382.6433 EKtot = 1829.5160 EPtot = -10212.1593 + BOND = 21.4426 ANGLE = 61.6042 DIHED = 78.3466 + 1-4 NB = 31.2549 1-4 EEL = 525.8436 VDWAALS = 1431.8360 + EELEC = -12362.5003 EHBOND = 0.0000 RESTRAINT = 0.0130 + EAMBER (non-restraint) = -10212.1723 + Ewald error estimate: 0.1249E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.013 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 292.05 PRESS = 0.0 + Etot = -8388.0484 EKtot = 1846.9753 EPtot = -10235.0237 + BOND = 28.3124 ANGLE = 68.7036 DIHED = 77.2483 + 1-4 NB = 29.1650 1-4 EEL = 524.7526 VDWAALS = 1417.4880 + EELEC = -12380.7112 EHBOND = 0.0000 RESTRAINT = 0.0176 + EAMBER (non-restraint) = -10235.0413 + Ewald error estimate: 0.2977E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 287.83 PRESS = 0.0 + Etot = -8395.2055 EKtot = 1820.3135 EPtot = -10215.5190 + BOND = 25.2842 ANGLE = 73.3605 DIHED = 70.6626 + 1-4 NB = 31.5238 1-4 EEL = 518.2658 VDWAALS = 1398.0348 + EELEC = -12332.6731 EHBOND = 0.0000 RESTRAINT = 0.0224 + EAMBER (non-restraint) = -10215.5414 + Ewald error estimate: 0.1576E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.022 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 282.50 PRESS = 0.0 + Etot = -8399.9898 EKtot = 1786.6255 EPtot = -10186.6153 + BOND = 33.6037 ANGLE = 60.0990 DIHED = 78.8605 + 1-4 NB = 34.6314 1-4 EEL = 542.7806 VDWAALS = 1481.7789 + EELEC = -12418.3922 EHBOND = 0.0000 RESTRAINT = 0.0226 + EAMBER (non-restraint) = -10186.6379 + Ewald error estimate: 0.2541E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.023 + BBMD : 0.000 STSM : 0.000 +=============================================================================== +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines, Average for All Tasks: +| +| Routine Sec % +| ------------------------------ +| DataDistrib 0.03 2.32 +| Nonbond 1.01 89.74 +| Bond 0.00 0.04 +| Angle 0.00 0.09 +| Dihedral 0.01 0.54 +| Shake 0.00 0.27 +| RunMD 0.07 6.34 +| Other 0.01 0.67 +| ------------------------------ +| Total 1.12 + +| PME Nonbond Pairlist CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.09 +| Build List 0.21 19.10 +| --------------------------------- +| Total 0.21 19.19 + +| PME Direct Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.52 46.10 +| Exclude Masked 0.01 0.71 +| Other 0.01 0.54 +| --------------------------------- +| Total 0.53 47.34 + +| PME Reciprocal Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.03 3.03 +| Grid Charges 0.02 1.47 +| Scalar Sum 0.04 3.79 +| Gradient Sum 0.03 3.08 +| FFT 0.13 11.82 +| --------------------------------- +| Total 0.26 23.20 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 + +| Final Performance Info: +| ----------------------------------------------------- +| Average timings for last 45 steps: +| Elapsed(s) = 0.99 Per Step(ms) = 22.08 +| ns/day = 7.82 seconds/ns = 11041.58 +| +| Average timings for all steps: +| Elapsed(s) = 1.12 Per Step(ms) = 22.45 +| ns/day = 7.70 seconds/ns = 11223.91 +| ----------------------------------------------------- + +| Master Setup CPU time: 0.07 seconds +| Master NonSetup CPU time: 1.12 seconds +| Master Total CPU time: 1.19 seconds 0.00 hours + +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds +| Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/abremd/save.pmemd/mdout.3 test/nfe/abremd/save.pmemd/mdout.3 new file mode 100644 index 0000000000..73d0d5d05e --- /dev/null +++ test/nfe/abremd/save.pmemd/mdout.3 @@ -0,0 +1,445 @@ + + ------------------------------------------------------- + Amber 18 PMEMD 2018 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 18 + +| Run on 09/21/2018 at 19:22:17 + +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abremd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output + +File Assignments: +| MDIN: mdin.3 +| MDOUT: mdout.3 +| INPCRD: inpcrd.3 +| PARM: prmtop +| RESTRT: restrt.3 +| REFC: refc +| MDVEL: mdvel.002 +| MDEN: mden.002 +| MDCRD: mdcrd.3 +| MDINFO: /dev/null +|LOGFILE: logfile.002 +| MDFRC: mdfrc.002 + + + Here is the input file: + + + &cntrl + igb = 0, ntx = 7, irest = 1, + ntb = 1, ntp = 0, temp0 = 320.0, + ntt = 3, gamma_ln = 1.0, + ntf = 2, ntc = 2, tol = 0.00001, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, + numexchg = 10 + / + + &abmd + monitor_file = 'abmd.3.txt' + monitor_freq = 3 + + umbrella_file = 'umbrella.3.nc' + + mode = 'FLOODING' + + timescale = 4.0 + + cv_file = 'cv.in' + / + + +| irandom = 1, using AMBER's internal random number generator (default). + + +| Conditional Compilation Defines Used: +| MPI +| PUBFFT +| BINTRAJ +| EMIL + +| Largest sphere to fit in unit cell has radius = 14.075 + +| New format PARM file being parsed. +| Version = 1.000 Date = 09/01/07 Time = 11:29:05 + +| Note: 1-4 EEL scale factors were NOT found in the topology file. +| Using default value of 1.2. + +| Note: 1-4 VDW scale factors were NOT found in the topology file. +| Using default value of 2.0. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 + NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 + NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 + NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 + NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 + IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 6 6 6 +| Direct force subcell size = 5.7460 5.7460 5.7460 + + BOX TYPE: TRUNCATED OCTAHEDRON + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + +NGLY + +General flags: + imin = 0, nmropt = 0 + +Replica exchange + numexchg= 10, rem= 3 + +Nature and format of input: + ntx = 7, irest = 1, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 5, ntrx = 1, ntwr = 50 + iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 2, ntb = 1, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 0 + +Molecular dynamics: + nstlim = 5, nscm = 1000, nrespa = 1 + t = 0.00000, dt = 0.00200, vlimit = 20.00000 + +Langevin dynamics temperature regulation: + ig = 71277 + temp0 = 320.00000, tempi = 0.00000, gamma_ln= 1.00000 + +SHAKE: + ntc = 2, jfastw = 0 + tol = 0.00001 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 5 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 1 + Box X = 34.476 Box Y = 34.476 Box Z = 34.476 + Alpha = 109.471 Beta = 109.471 Gamma = 109.471 + NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + +NGLY + begin time read from input coords = 0.000 ps + + + Number of triangulated 3-point waters found: 1001 + + Sum of charges from parm topology file = -0.00000001 + Forcing neutrality... + +| Dynamic Memory, Types Used: +| Reals 245730 +| Integers 211573 + +| Nonbonded Pairs Initial Allocation: 358302 + +| Running AMBER/MPI version on 2 MPI task + + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + --------------------------------------------------- + APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION + using 5000.0 points per unit in tabled values + TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff +| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 +| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 + --------------------------------------------------- +|--------------------------------------------------- +| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.47 +| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.89 +|--------------------------------------------------- + + NFE : () () () () () () () () () () A. B. M. D. () () () () () () () () () + NFE : + NFE : mode = FLOODING + NFE : + NFE : CV #1 + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : monitor_file = abmd.3.txt + NFE : monitor_freq = 3 (0.0060 ps) + NFE : umbrella_file = umbrella.3.nc (not found) + NFE : + NFE : umbrella discretization (new) : + NFE : CV #1 not periodic, 97 points, min/max = 0.000000/12.000000 + NFE : + NFE : flooding timescale = 4.000 ps + NFE : + NFE : () () () () () () () () () () () () () () () () () () () () () () () () + + + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 309.88 PRESS = 0.0 + Etot = -8148.4280 EKtot = 1959.7460 EPtot = -10108.1740 + BOND = 28.5765 ANGLE = 66.3283 DIHED = 73.9458 + 1-4 NB = 29.5050 1-4 EEL = 526.9483 VDWAALS = 1332.3812 + EELEC = -12165.8610 EHBOND = 0.0000 RESTRAINT = 0.0020 + EAMBER (non-restraint) = -10108.1760 + Ewald error estimate: 0.1892E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.002 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 318.79 PRESS = 0.0 + Etot = -8058.6964 EKtot = 2016.1167 EPtot = -10074.8130 + BOND = 33.1863 ANGLE = 71.4355 DIHED = 79.8458 + 1-4 NB = 33.5735 1-4 EEL = 534.0248 VDWAALS = 1428.4767 + EELEC = -12255.3573 EHBOND = 0.0000 RESTRAINT = 0.0015 + EAMBER (non-restraint) = -10074.8145 + Ewald error estimate: 0.8594E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.001 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 324.59 PRESS = 0.0 + Etot = -8058.1300 EKtot = 2052.7870 EPtot = -10110.9170 + BOND = 24.5371 ANGLE = 73.3636 DIHED = 73.8941 + 1-4 NB = 32.7485 1-4 EEL = 541.6066 VDWAALS = 1431.8271 + EELEC = -12288.8979 EHBOND = 0.0000 RESTRAINT = 0.0040 + EAMBER (non-restraint) = -10110.9210 + Ewald error estimate: 0.5370E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.004 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 321.25 PRESS = 0.0 + Etot = -8043.2866 EKtot = 2031.6912 EPtot = -10074.9779 + BOND = 31.7722 ANGLE = 75.1007 DIHED = 78.2022 + 1-4 NB = 36.1719 1-4 EEL = 543.1064 VDWAALS = 1417.2884 + EELEC = -12256.6261 EHBOND = 0.0000 RESTRAINT = 0.0065 + EAMBER (non-restraint) = -10074.9843 + Ewald error estimate: 0.3465E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.006 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 317.84 PRESS = 0.0 + Etot = -8049.6246 EKtot = 2010.1250 EPtot = -10059.7496 + BOND = 31.8399 ANGLE = 61.3675 DIHED = 82.6976 + 1-4 NB = 33.4875 1-4 EEL = 541.5646 VDWAALS = 1413.3763 + EELEC = -12224.0919 EHBOND = 0.0000 RESTRAINT = 0.0089 + EAMBER (non-restraint) = -10059.7585 + Ewald error estimate: 0.3124E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.009 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 306.46 PRESS = 0.0 + Etot = -8136.8326 EKtot = 1938.0955 EPtot = -10074.9280 + BOND = 34.4842 ANGLE = 65.1103 DIHED = 74.6808 + 1-4 NB = 31.1545 1-4 EEL = 515.1709 VDWAALS = 1290.7523 + EELEC = -12086.2851 EHBOND = 0.0000 RESTRAINT = 0.0040 + EAMBER (non-restraint) = -10074.9320 + Ewald error estimate: 0.3167E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.004 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 310.06 PRESS = 0.0 + Etot = -8136.6530 EKtot = 1960.9140 EPtot = -10097.5670 + BOND = 18.2605 ANGLE = 58.2778 DIHED = 78.5227 + 1-4 NB = 30.4290 1-4 EEL = 534.5778 VDWAALS = 1278.1400 + EELEC = -12095.7811 EHBOND = 0.0000 RESTRAINT = 0.0064 + EAMBER (non-restraint) = -10097.5734 + Ewald error estimate: 0.2049E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.006 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 306.07 PRESS = 0.0 + Etot = -8132.1081 EKtot = 1935.6321 EPtot = -10067.7402 + BOND = 22.7527 ANGLE = 60.6712 DIHED = 76.6262 + 1-4 NB = 32.0402 1-4 EEL = 533.5930 VDWAALS = 1287.2367 + EELEC = -12080.6689 EHBOND = 0.0000 RESTRAINT = 0.0087 + EAMBER (non-restraint) = -10067.7489 + Ewald error estimate: 0.1371E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.009 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 307.79 PRESS = 0.0 + Etot = -8130.1906 EKtot = 1946.5191 EPtot = -10076.7097 + BOND = 30.2595 ANGLE = 68.2161 DIHED = 70.8370 + 1-4 NB = 29.3837 1-4 EEL = 529.2475 VDWAALS = 1309.3363 + EELEC = -12114.0009 EHBOND = 0.0000 RESTRAINT = 0.0110 + EAMBER (non-restraint) = -10076.7207 + Ewald error estimate: 0.1146E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.011 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 307.27 PRESS = 0.0 + Etot = -8130.2841 EKtot = 1943.2768 EPtot = -10073.5609 + BOND = 27.5660 ANGLE = 62.2577 DIHED = 74.7710 + 1-4 NB = 33.7953 1-4 EEL = 542.2518 VDWAALS = 1336.2511 + EELEC = -12150.4673 EHBOND = 0.0000 RESTRAINT = 0.0135 + EAMBER (non-restraint) = -10073.5744 + Ewald error estimate: 0.8009E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.013 + BBMD : 0.000 STSM : 0.000 +=============================================================================== +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines, Average for All Tasks: +| +| Routine Sec % +| ------------------------------ +| DataDistrib 0.02 1.56 +| Nonbond 1.02 91.12 +| Bond 0.00 0.00 +| Angle 0.00 0.18 +| Dihedral 0.01 0.76 +| Shake 0.00 0.18 +| RunMD 0.06 5.53 +| Other 0.01 0.67 +| ------------------------------ +| Total 1.12 + +| PME Nonbond Pairlist CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.18 +| Build List 0.23 20.16 +| --------------------------------- +| Total 0.23 20.34 + +| PME Direct Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.52 46.30 +| Exclude Masked 0.01 0.67 +| Other 0.01 0.62 +| --------------------------------- +| Total 0.53 47.59 + +| PME Reciprocal Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.03 2.81 +| Grid Charges 0.02 1.65 +| Scalar Sum 0.04 3.75 +| Gradient Sum 0.03 2.85 +| FFT 0.14 12.09 +| --------------------------------- +| Total 0.26 23.15 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 + +| Final Performance Info: +| ----------------------------------------------------- +| Average timings for last 45 steps: +| Elapsed(s) = 0.99 Per Step(ms) = 22.08 +| ns/day = 7.82 seconds/ns = 11042.23 +| +| Average timings for all steps: +| Elapsed(s) = 1.12 Per Step(ms) = 22.45 +| ns/day = 7.70 seconds/ns = 11224.66 +| ----------------------------------------------------- + +| Master Setup CPU time: 0.07 seconds +| Master NonSetup CPU time: 1.12 seconds +| Master Total CPU time: 1.19 seconds 0.00 hours + +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds +| Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/abremd/save.pmemd/mdout.4 test/nfe/abremd/save.pmemd/mdout.4 new file mode 100644 index 0000000000..f7a707aa0a --- /dev/null +++ test/nfe/abremd/save.pmemd/mdout.4 @@ -0,0 +1,445 @@ + + ------------------------------------------------------- + Amber 18 PMEMD 2018 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 18 + +| Run on 09/21/2018 at 19:22:17 + +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abremd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output + +File Assignments: +| MDIN: mdin.4 +| MDOUT: mdout.4 +| INPCRD: inpcrd.4 +| PARM: prmtop +| RESTRT: restrt.4 +| REFC: refc +| MDVEL: mdvel.003 +| MDEN: mden.003 +| MDCRD: mdcrd.4 +| MDINFO: /dev/null +|LOGFILE: logfile.003 +| MDFRC: mdfrc.003 + + + Here is the input file: + + + &cntrl + igb = 0, ntx = 7, irest = 1, + ntb = 1, ntp = 0, temp0 = 330.0, + ntt = 3, gamma_ln = 1.0, + ntf = 2, ntc = 2, tol = 0.00001, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, + numexchg = 10 + / + + &abmd + monitor_file = 'abmd.4.txt' + monitor_freq = 5 + + umbrella_file = 'umbrella.4.nc' + + mode = 'FLOODING' + + timescale = 1.0 + + cv_file = 'cv.in' + / + + +| irandom = 1, using AMBER's internal random number generator (default). + + +| Conditional Compilation Defines Used: +| MPI +| PUBFFT +| BINTRAJ +| EMIL + +| Largest sphere to fit in unit cell has radius = 14.075 + +| New format PARM file being parsed. +| Version = 1.000 Date = 09/01/07 Time = 11:29:05 + +| Note: 1-4 EEL scale factors were NOT found in the topology file. +| Using default value of 1.2. + +| Note: 1-4 VDW scale factors were NOT found in the topology file. +| Using default value of 2.0. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 + NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 + NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 + NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 + NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 + IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 6 6 6 +| Direct force subcell size = 5.7460 5.7460 5.7460 + + BOX TYPE: TRUNCATED OCTAHEDRON + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + +NGLY + +General flags: + imin = 0, nmropt = 0 + +Replica exchange + numexchg= 10, rem= 3 + +Nature and format of input: + ntx = 7, irest = 1, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 5, ntrx = 1, ntwr = 50 + iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 2, ntb = 1, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 0 + +Molecular dynamics: + nstlim = 5, nscm = 1000, nrespa = 1 + t = 0.00000, dt = 0.00200, vlimit = 20.00000 + +Langevin dynamics temperature regulation: + ig = 71277 + temp0 = 330.00000, tempi = 0.00000, gamma_ln= 1.00000 + +SHAKE: + ntc = 2, jfastw = 0 + tol = 0.00001 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 5 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 1 + Box X = 34.476 Box Y = 34.476 Box Z = 34.476 + Alpha = 109.471 Beta = 109.471 Gamma = 109.471 + NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + +NGLY + begin time read from input coords = 0.000 ps + + + Number of triangulated 3-point waters found: 1001 + + Sum of charges from parm topology file = -0.00000001 + Forcing neutrality... + +| Dynamic Memory, Types Used: +| Reals 245716 +| Integers 210016 + +| Nonbonded Pairs Initial Allocation: 358302 + +| Running AMBER/MPI version on 2 MPI task + + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + --------------------------------------------------- + APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION + using 5000.0 points per unit in tabled values + TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff +| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 +| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 + --------------------------------------------------- +|--------------------------------------------------- +| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.47 +| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.89 +|--------------------------------------------------- + + NFE : () () () () () () () () () () A. B. M. D. () () () () () () () () () + NFE : + NFE : mode = FLOODING + NFE : + NFE : CV #1 + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : monitor_file = abmd.4.txt + NFE : monitor_freq = 5 (0.0100 ps) + NFE : umbrella_file = umbrella.4.nc (not found) + NFE : + NFE : umbrella discretization (new) : + NFE : CV #1 not periodic, 97 points, min/max = 0.000000/12.000000 + NFE : + NFE : flooding timescale = 1.000 ps + NFE : + NFE : () () () () () () () () () () () () () () () () () () () () () () () () + + + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 329.71 PRESS = 0.0 + Etot = -7998.9503 EKtot = 2085.1752 EPtot = -10084.1255 + BOND = 22.6133 ANGLE = 66.3319 DIHED = 76.2142 + 1-4 NB = 33.3360 1-4 EEL = 538.5129 VDWAALS = 1420.1963 + EELEC = -12241.3364 EHBOND = 0.0000 RESTRAINT = 0.0064 + EAMBER (non-restraint) = -10084.1319 + Ewald error estimate: 0.9435E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.006 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 310.83 PRESS = 0.0 + Etot = -8085.8309 EKtot = 1965.7838 EPtot = -10051.6147 + BOND = 34.5544 ANGLE = 60.0475 DIHED = 76.6088 + 1-4 NB = 30.9082 1-4 EEL = 526.4871 VDWAALS = 1341.2369 + EELEC = -12121.4636 EHBOND = 0.0000 RESTRAINT = 0.0060 + EAMBER (non-restraint) = -10051.6207 + Ewald error estimate: 0.9334E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.006 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 315.65 PRESS = 0.0 + Etot = -8067.8457 EKtot = 1996.2698 EPtot = -10064.1155 + BOND = 36.0130 ANGLE = 55.6940 DIHED = 77.3167 + 1-4 NB = 29.7730 1-4 EEL = 521.2952 VDWAALS = 1336.9267 + EELEC = -12121.1498 EHBOND = 0.0000 RESTRAINT = 0.0158 + EAMBER (non-restraint) = -10064.1313 + Ewald error estimate: 0.1166E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.016 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 312.60 PRESS = 0.0 + Etot = -8063.9979 EKtot = 1976.9513 EPtot = -10040.9493 + BOND = 27.2003 ANGLE = 62.6683 DIHED = 78.5402 + 1-4 NB = 32.1308 1-4 EEL = 522.5826 VDWAALS = 1319.6565 + EELEC = -12083.7532 EHBOND = 0.0000 RESTRAINT = 0.0253 + EAMBER (non-restraint) = -10040.9746 + Ewald error estimate: 0.1116E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.025 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 314.42 PRESS = 0.0 + Etot = -8078.5146 EKtot = 1988.4975 EPtot = -10067.0121 + BOND = 23.1026 ANGLE = 67.4259 DIHED = 72.7501 + 1-4 NB = 30.3897 1-4 EEL = 523.6900 VDWAALS = 1306.9267 + EELEC = -12091.3321 EHBOND = 0.0000 RESTRAINT = 0.0349 + EAMBER (non-restraint) = -10067.0470 + Ewald error estimate: 0.7390E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.035 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 320.17 PRESS = 0.0 + Etot = -7987.2830 EKtot = 2024.8462 EPtot = -10012.1292 + BOND = 30.8420 ANGLE = 61.4213 DIHED = 85.7582 + 1-4 NB = 36.2938 1-4 EEL = 537.9794 VDWAALS = 1432.0555 + EELEC = -12196.4950 EHBOND = 0.0000 RESTRAINT = 0.0157 + EAMBER (non-restraint) = -10012.1449 + Ewald error estimate: 0.1312E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.016 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 314.71 PRESS = 0.0 + Etot = -7985.6242 EKtot = 1990.2847 EPtot = -9975.9089 + BOND = 31.0696 ANGLE = 66.2423 DIHED = 78.3173 + 1-4 NB = 36.6610 1-4 EEL = 540.0589 VDWAALS = 1424.3550 + EELEC = -12152.6381 EHBOND = 0.0000 RESTRAINT = 0.0251 + EAMBER (non-restraint) = -9975.9340 + Ewald error estimate: 0.1265E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.025 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 311.83 PRESS = 0.0 + Etot = -7988.9275 EKtot = 1972.0752 EPtot = -9961.0027 + BOND = 25.9141 ANGLE = 70.6956 DIHED = 80.0198 + 1-4 NB = 38.9425 1-4 EEL = 535.0755 VDWAALS = 1375.5478 + EELEC = -12087.2325 EHBOND = 0.0000 RESTRAINT = 0.0345 + EAMBER (non-restraint) = -9961.0372 + Ewald error estimate: 0.6147E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.035 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 314.72 PRESS = 0.0 + Etot = -7989.3351 EKtot = 1990.3716 EPtot = -9979.7067 + BOND = 26.3346 ANGLE = 77.2965 DIHED = 76.4488 + 1-4 NB = 38.0978 1-4 EEL = 537.1932 VDWAALS = 1329.8156 + EELEC = -12064.9377 EHBOND = 0.0000 RESTRAINT = 0.0443 + EAMBER (non-restraint) = -9979.7510 + Ewald error estimate: 0.5486E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.044 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 320.97 PRESS = 0.0 + Etot = -8001.7956 EKtot = 2029.8642 EPtot = -10031.6597 + BOND = 25.6569 ANGLE = 67.5005 DIHED = 72.4776 + 1-4 NB = 35.4194 1-4 EEL = 538.0290 VDWAALS = 1314.7280 + EELEC = -12085.5256 EHBOND = 0.0000 RESTRAINT = 0.0543 + EAMBER (non-restraint) = -10031.7140 + Ewald error estimate: 0.7120E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.054 + BBMD : 0.000 STSM : 0.000 +=============================================================================== +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines, Average for All Tasks: +| +| Routine Sec % +| ------------------------------ +| DataDistrib 0.03 2.45 +| Nonbond 1.01 90.50 +| Bond 0.00 0.00 +| Angle 0.00 0.22 +| Dihedral 0.00 0.36 +| Shake 0.00 0.13 +| RunMD 0.06 5.75 +| Other 0.01 0.58 +| ------------------------------ +| Total 1.12 + +| PME Nonbond Pairlist CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.09 +| Build List 0.22 19.22 +| --------------------------------- +| Total 0.22 19.31 + +| PME Direct Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.52 46.43 +| Exclude Masked 0.01 0.89 +| Other 0.01 0.67 +| --------------------------------- +| Total 0.54 47.99 + +| PME Reciprocal Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.03 2.90 +| Grid Charges 0.02 1.56 +| Scalar Sum 0.04 4.01 +| Gradient Sum 0.03 2.77 +| FFT 0.13 11.91 +| --------------------------------- +| Total 0.26 23.15 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 + +| Final Performance Info: +| ----------------------------------------------------- +| Average timings for last 45 steps: +| Elapsed(s) = 0.99 Per Step(ms) = 22.09 +| ns/day = 7.82 seconds/ns = 11043.07 +| +| Average timings for all steps: +| Elapsed(s) = 1.12 Per Step(ms) = 22.45 +| ns/day = 7.70 seconds/ns = 11224.41 +| ----------------------------------------------------- + +| Master Setup CPU time: 0.07 seconds +| Master NonSetup CPU time: 1.12 seconds +| Master Total CPU time: 1.19 seconds 0.00 hours + +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds +| Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/abremd/save.pmemd/rem.log test/nfe/abremd/save.pmemd/rem.log new file mode 100644 index 0000000000..8a2c251800 --- /dev/null +++ test/nfe/abremd/save.pmemd/rem.log @@ -0,0 +1,56 @@ +# Replica Exchange log file +# numexchg is 10 +# REMD filenames: +# remlog= rem.log +# remtype= rem.type +# Rep#, Neibr#, Temp0, PotE(x_1), PotE(x_2), left_fe, right_fe, Success, Success rate (i,i+1) +# exchange 1 + 1 4 300.00 -10152.55 -10184.84 -0.00 0.00 T 0.00 + 2 3 310.00 -10313.68 -10131.41 0.00 0.00 F 0.00 + 3 2 320.00 -10131.41 -10313.68 -0.00 0.00 F 0.00 + 4 1 330.00 -10184.84 -10152.55 0.00 -0.00 T 2.00 +# exchange 2 + 1 2 300.00 -10291.32 -10313.84 -0.00 0.01 T 1.00 + 2 1 310.00 -10313.84 -10291.33 0.00 0.00 T 0.00 + 3 4 320.00 -10095.27 -10055.89 -0.00 0.00 T 1.00 + 4 3 330.00 -10055.88 -10095.27 0.01 -0.00 T 1.00 +# exchange 3 + 1 4 300.00 -10289.45 -10051.82 0.00 0.01 F 0.67 + 2 3 310.00 -10225.31 -10094.44 0.00 0.00 F 0.00 + 3 2 320.00 -10094.44 -10225.31 0.00 0.00 F 0.67 + 4 1 330.00 -10051.81 -10289.46 0.01 0.00 F 0.67 +# exchange 4 + 1 2 300.00 -10265.73 -10206.90 0.00 0.01 F 0.50 + 2 1 310.00 -10206.90 -10265.74 0.00 0.00 F 0.00 + 3 4 320.00 -10099.75 -10050.52 0.00 -0.00 F 0.50 + 4 3 330.00 -10050.51 -10099.74 0.01 0.00 F 0.50 +# exchange 5 + 1 4 300.00 -10300.04 -10043.43 0.01 0.01 F 0.40 + 2 3 310.00 -10208.61 -10079.60 0.00 0.01 F 0.00 + 3 2 320.00 -10079.59 -10208.63 0.00 -0.00 F 0.40 + 4 1 330.00 -10043.40 -10300.06 0.01 0.01 F 0.40 +# exchange 6 + 1 2 300.00 -10260.88 -10235.22 0.01 0.02 T 0.67 + 2 1 310.00 -10235.21 -10260.91 0.00 0.01 T 0.00 + 3 4 320.00 -10055.90 -10067.56 0.00 -0.00 T 0.67 + 4 3 330.00 -10067.53 -10055.90 0.02 0.01 T 0.33 +# exchange 7 + 1 4 300.00 -10252.58 -10006.47 0.01 0.02 F 0.57 + 2 3 310.00 -10220.98 -10083.99 0.00 0.01 F 0.00 + 3 2 320.00 -10083.98 -10220.99 0.00 -0.00 F 0.57 + 4 1 330.00 -10006.45 -10252.59 0.02 0.01 F 0.29 +# exchange 8 + 1 2 300.00 -10287.32 -10214.16 0.01 0.02 F 0.50 + 2 1 310.00 -10214.18 -10287.33 -0.00 0.01 F 0.00 + 3 4 320.00 -10080.96 -9981.16 0.00 -0.01 F 0.50 + 4 3 330.00 -9981.14 -10080.93 0.02 0.01 F 0.25 +# exchange 9 + 1 4 300.00 -10235.26 -9966.66 0.02 0.02 F 0.44 + 2 3 310.00 -10239.90 -10078.44 -0.00 0.01 F 0.00 + 3 2 320.00 -10078.43 -10239.92 0.00 -0.01 F 0.44 + 4 1 330.00 -9966.62 -10235.29 0.02 0.02 F 0.22 +# exchange 10 + 1 2 300.00 -10277.11 -10214.15 0.02 0.02 T 0.60 + 2 1 310.00 -10214.16 -10277.14 -0.00 0.01 T 0.00 + 3 4 320.00 -10067.13 -9991.05 0.00 -0.01 F 0.40 + 4 3 330.00 -9991.02 -10067.11 0.02 0.02 F 0.20 diff --git test/nfe/abremd/save.pmemd/umbrella.1.ncdump test/nfe/abremd/save.pmemd/umbrella.1.ncdump new file mode 100644 index 0000000000..cf81b0755f --- /dev/null +++ test/nfe/abremd/save.pmemd/umbrella.1.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0196763007, 0.0557376548, 0.0458989705, + 0.0070496982, 0.0015711845, 0.0000484932, 0.0000000000, + 0.0000000000, 0.0078577012, 0.0447327655, 0.0508991038, + 0.0164112318, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/abremd/save.pmemd/umbrella.2.ncdump test/nfe/abremd/save.pmemd/umbrella.2.ncdump new file mode 100644 index 0000000000..7a83af83a6 --- /dev/null +++ test/nfe/abremd/save.pmemd/umbrella.2.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0076373389, 0.0259665310, 0.0229775637, + 0.0035041735, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0080930784, 0.0267834529, 0.0247803590, + 0.0052711269, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/abremd/save.pmemd/umbrella.3.ncdump test/nfe/abremd/save.pmemd/umbrella.3.ncdump new file mode 100644 index 0000000000..564b827648 --- /dev/null +++ test/nfe/abremd/save.pmemd/umbrella.3.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0043979188, + 0.0113317005, 0.0085911359, 0.0006554006, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0017123156, + 0.0120885698, 0.0163446943, 0.0072171248, 0.0000101385, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/abremd/save.pmemd/umbrella.4.ncdump test/nfe/abremd/save.pmemd/umbrella.4.ncdump new file mode 100644 index 0000000000..193983fed2 --- /dev/null +++ test/nfe/abremd/save.pmemd/umbrella.4.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0005518314, 0.0021255408, 0.0138612530, + 0.0574268184, 0.0600261454, 0.0160744929, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0086074340, + 0.0401974734, 0.0412491474, 0.0100648674, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/abremd/save/abmd.1.txt test/nfe/abremd/save/abmd.1.txt index cdc438251c..46a196f20f 100644 --- test/nfe/abremd/save/abmd.1.txt +++ test/nfe/abremd/save/abmd.1.txt @@ -1,63 +1,53 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0000 7.3651005026 0.0000000000 - 0.0020 7.3639106649 0.0019989640 - 0.0040 7.3628072820 0.0039973681 - 0.0060 7.3615511491 0.0059948433 - 0.0080 7.3600886260 0.0079907714 - 0.0100 7.3582942462 0.0099838954 - 0.0100 7.3582942462 0.0119819335 - 0.0120 7.3562908288 0.0139705873 - 0.0140 7.3541195256 0.0159536209 - 0.0160 7.3518069947 0.0179296605 - 0.0180 7.3494900459 0.0198988487 - 0.0200 7.3473288043 0.0218631899 - 0.0200 7.3473288043 0.0238588421 - 0.0220 7.3453301949 0.0258186812 - 0.0240 7.3433855773 0.0277729350 - 0.0260 7.3414418366 0.0297204071 - 0.0280 7.3396347421 0.0316647623 - 0.0300 7.3378472822 0.0336032712 - 0.0300 7.3378472822 0.0355968861 - 0.0320 7.3357875612 0.0375182119 - 0.0340 7.3335168272 0.0394212709 - 0.0360 7.3309211226 0.0412971518 - 0.0380 7.3281116581 0.0431458361 - 0.0400 7.3251114447 0.0449641484 - 0.0400 7.3251114447 0.0469557317 - 0.0420 7.3219278592 0.0487387765 - 0.0440 7.3185276287 0.0504789356 - 0.0460 7.3149809548 0.0521761774 - 0.0480 7.3113394138 0.0538309261 - 0.0500 7.3075233672 0.0554313520 - 0.0500 7.3075233672 0.0574223212 - 0.0520 7.3037825707 0.0589914229 - 0.0540 7.2999494134 0.0605085108 - 0.0560 7.2961781159 0.0619916029 - 0.0580 7.2923723398 0.0634275338 - 0.0600 7.2884756220 0.0648051988 - 0.0600 7.2884756220 0.0667985556 - 0.0620 7.2847758537 0.0681645451 - 0.0640 7.2813176162 0.0695319082 - 0.0660 7.2780435314 0.0708967455 - 0.0680 7.2747082907 0.0722130541 - 0.0700 7.2712748362 0.0734696248 - 0.0700 6.2764473425 0.0000000000 - 0.0720 6.2740633053 0.0009980722 - 0.0740 6.2719666414 0.0019962420 - 0.0760 6.2703253250 0.0029944093 - 0.0780 6.2696001812 0.0039928353 - 0.0800 6.2695847647 0.0049915520 - 0.0800 6.2695847647 0.0059902745 - 0.0820 6.2700688375 0.0069889832 - 0.0840 6.2707385471 0.0079873934 - 0.0860 6.2716030109 0.0089852343 - 0.0880 6.2722123280 0.0099828948 - 0.0900 6.2725968955 0.0109806435 - 0.0900 6.2725968955 0.0119790387 - 0.0920 6.2729272825 0.0129766883 - 0.0940 6.2732375426 0.0139742356 - 0.0960 6.2735826656 0.0149715251 - 0.0980 6.2741040696 0.0159679891 - 0.1000 6.2747782835 0.0169634063 + 0.0000 6.3043274285 0.0000000000 + 0.0020 6.3050206100 0.0019910867 + 0.0040 6.3057901435 0.0039819731 + 0.0060 6.3062800905 0.0059727849 + 0.0080 6.3065660468 0.0079636170 + 0.0100 7.3582826706 0.0000000000 + 0.0120 7.3563766915 0.0019974433 + 0.0140 7.3544212806 0.0039934117 + 0.0160 7.3526015860 0.0059877030 + 0.0180 7.3508913247 0.0079801915 + 0.0200 7.3494821558 0.0099716384 + 0.0220 7.3482350536 0.0119620434 + 0.0240 7.3469045246 0.0139502336 + 0.0260 7.3455287050 0.0159360002 + 0.0280 7.3440826824 0.0179187185 + 0.0300 7.3423779254 0.0198956888 + 0.0320 7.3405830241 0.0218673573 + 0.0340 7.3386706476 0.0238323393 + 0.0360 7.3366351159 0.0257892565 + 0.0380 7.3345235210 0.0277377180 + 0.0400 7.3322707438 0.0296748803 + 0.0420 7.3298517543 0.0315980078 + 0.0440 7.3272128804 0.0335026866 + 0.0460 7.3243089811 0.0353834557 + 0.0480 7.3211127662 0.0372341648 + 0.0500 6.2960172109 0.0099344594 + 0.0520 6.2949474771 0.0119213572 + 0.0540 6.2937894694 0.0139072806 + 0.0560 6.2927444668 0.0158932649 + 0.0580 6.2914880545 0.0178770280 + 0.0600 6.2902025992 0.0198593886 + 0.0620 6.2888743162 0.0218399438 + 0.0640 6.2874324609 0.0238175117 + 0.0660 6.2858398364 0.0257908064 + 0.0680 6.2839631872 0.0277564763 + 0.0700 6.2820400364 0.0297165495 + 0.0720 6.2801312258 0.0316715834 + 0.0740 6.2785853454 0.0336301496 + 0.0760 6.2772064955 0.0355894727 + 0.0780 6.2761396711 0.0375548838 + 0.0800 6.2754708919 0.0395307702 + 0.0820 6.2750651427 0.0415143177 + 0.0840 6.2747005161 0.0434989818 + 0.0860 6.2744438931 0.0454870159 + 0.0880 6.2742509119 0.0474770930 + 0.0900 7.2681871446 0.0341445304 + 0.0920 7.2671654575 0.0359976425 + 0.0940 7.2659405543 0.0378200736 + 0.0960 7.2643848522 0.0395916844 + 0.0980 7.2627946324 0.0413540101 diff --git test/nfe/abremd/save/abmd.2.txt test/nfe/abremd/save/abmd.2.txt index c3bc574a97..d840b634ed 100644 --- test/nfe/abremd/save/abmd.2.txt +++ test/nfe/abremd/save/abmd.2.txt @@ -1,33 +1,28 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0020 6.5187674057 0.0004994043 - 0.0060 6.5201274020 0.0014979328 - 0.0100 6.5219694165 0.0024957103 - 0.0120 6.5224516964 0.0034938060 - 0.0160 6.5228294655 0.0044918516 - 0.0200 6.5237213609 0.0054890973 - 0.0220 6.3024277823 0.0023772265 - 0.0260 6.3026452244 0.0043730368 - 0.0300 6.3018354317 0.0063476663 - 0.0320 6.3008599037 0.0083188994 - 0.0360 6.2990818803 0.0102731994 - 0.0400 6.2981423605 0.0122449126 - 0.0420 6.5500095710 0.0077742245 - 0.0460 6.5560572425 0.0085565232 - 0.0500 6.5619547959 0.0093423128 - 0.0520 6.5647601625 0.0102367880 - 0.0560 6.5701932505 0.0110331560 - 0.0600 6.5747271573 0.0118580604 - 0.0620 6.2841837219 0.0143727788 - 0.0660 6.2810447513 0.0162481131 - 0.0700 6.2764473425 0.0180598212 - 0.0720 7.2679850967 0.0019971715 - 0.0760 7.2613521917 0.0059884069 - 0.0800 7.2554580172 0.0099688120 - 0.0820 7.2533261193 0.0139566044 - 0.0860 7.2502122848 0.0179315620 - 0.0900 7.2472799154 0.0218972446 - 0.0920 7.2454025583 0.0258682217 - 0.0960 7.2411591487 0.0297792579 - 0.1000 7.2371562464 0.0336620967 + 0.0000 7.3651005026 0.0000000000 + 0.0040 7.3628045565 0.0019986832 + 0.0080 7.3600812668 0.0039953788 + 0.0120 6.3061202235 0.0009955169 + 0.0160 6.3048406029 0.0029865495 + 0.0200 6.3042728304 0.0049776261 + 0.0240 6.3049904094 0.0069687643 + 0.0280 6.3053960245 0.0089597501 + 0.0320 6.3043645923 0.0109510371 + 0.0360 6.3020994665 0.0129405170 + 0.0400 6.3000373817 0.0149274288 + 0.0440 6.2985572521 0.0169138888 + 0.0480 6.2969907254 0.0188982461 + 0.0520 7.3139795257 0.0056469779 + 0.0560 7.3064792124 0.0075294006 + 0.0600 7.2991681892 0.0093946252 + 0.0640 7.2931096436 0.0112638690 + 0.0680 7.2882013884 0.0131429099 + 0.0720 7.2833102796 0.0150082023 + 0.0760 7.2781439761 0.0168483368 + 0.0800 7.2733041441 0.0186792059 + 0.0840 7.2705127577 0.0205710693 + 0.0880 7.2690748715 0.0225113423 + 0.0920 6.2747016802 0.0205098262 + 0.0960 6.2769585712 0.0225677660 diff --git test/nfe/abremd/save/abmd.3.txt test/nfe/abremd/save/abmd.3.txt index 24219a6df9..59d4910a54 100644 --- test/nfe/abremd/save/abmd.3.txt +++ test/nfe/abremd/save/abmd.3.txt @@ -1,23 +1,20 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0040 6.3057889791 0.0019909905 - 0.0100 6.3053882494 0.0049776605 - 0.0140 6.3037619004 0.0079641965 - 0.0200 6.3023530845 0.0109501700 - 0.0240 6.5261579948 0.0033100348 - 0.0300 6.5325322957 0.0045828887 - 0.0340 6.5376716231 0.0059044522 - 0.0400 6.5468945796 0.0070948284 - 0.0440 6.2969086744 0.0149851652 - 0.0500 6.2930801523 0.0178868363 - 0.0540 6.2896795459 0.0207901188 - 0.0600 6.2854252731 0.0236585813 - 0.0640 6.5787531704 0.0081996249 - 0.0700 6.5846486271 0.0094291697 - 0.0740 6.5890681678 0.0107279432 - 0.0800 6.5928806280 0.0120544258 - 0.0840 6.5930179190 0.0135443391 - 0.0900 6.5923007095 0.0150719774 - 0.0940 6.5924315624 0.0165621443 - 0.1000 6.5904950825 0.0181419345 + 0.0000 8.0143490198 0.0000000000 + 0.0060 8.0227202554 0.0014959505 + 0.0120 6.5220462551 0.0004992275 + 0.0180 6.5216696966 0.0019969911 + 0.0240 6.5228357389 0.0034941996 + 0.0300 6.5271371661 0.0049862650 + 0.0360 6.5332072817 0.0064648904 + 0.0420 6.5389189266 0.0079303987 + 0.0480 6.5453435168 0.0093733340 + 0.0540 8.0935890307 0.0031308547 + 0.0600 8.1016800810 0.0045502021 + 0.0660 8.1095587076 0.0059592236 + 0.0720 8.1125659325 0.0074195384 + 0.0780 8.1188605473 0.0088262882 + 0.0840 8.1281035780 0.0101529329 + 0.0900 8.1318012662 0.0115691879 + 0.0960 8.1309086392 0.0130899366 diff --git test/nfe/abremd/save/abmd.4.txt test/nfe/abremd/save/abmd.4.txt index b0b58c0009..5fb97027b2 100644 --- test/nfe/abremd/save/abmd.4.txt +++ test/nfe/abremd/save/abmd.4.txt @@ -1,13 +1,13 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0080 8.0262697633 0.0079675960 - 0.0180 8.0437643129 0.0197296134 - 0.0280 8.0647591509 0.0309560757 - 0.0380 8.0841185755 0.0416119335 - 0.0480 8.0944178733 0.0525827116 - 0.0580 8.1040466240 0.0633795568 - 0.0680 8.1165439187 0.0733792625 - 0.0780 8.1240118459 0.0838899934 - 0.0880 8.1349136175 0.0932263438 - 0.0980 8.1338437757 0.1055102849 + 0.0000 6.5186874308 0.0000000000 + 0.0100 8.0297471498 0.0000000000 + 0.0200 8.0462771726 0.0099277469 + 0.0300 8.0665383193 0.0196005978 + 0.0400 8.0820788995 0.0290587048 + 0.0500 6.5481062613 0.0097344951 + 0.0600 6.5633227724 0.0193564990 + 0.0700 6.5778885731 0.0287743413 + 0.0800 6.5880050831 0.0381911254 + 0.0900 6.5895454765 0.0480621416 diff --git test/nfe/abremd/save/mdout.1 test/nfe/abremd/save/mdout.1 index 76db5f7451..3fb2013684 100644 --- test/nfe/abremd/save/mdout.1 +++ test/nfe/abremd/save/mdout.1 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/14/2016 at 18:10:29 +| Run on 09/21/2018 at 19:19:01 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/abremd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abremd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -45,8 +45,8 @@ File Assignments: ntb = 1, ntp = 0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, - ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, numexchg = 10 / @@ -90,8 +90,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -113,7 +113,7 @@ General flags: imin = 0, nmropt = 0 Replica exchange - numexchg= 10, rem= 1 + numexchg= 10, rem= 3 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 @@ -165,18 +165,43 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- + + NFE : () () () () () () () () () () A. B. M. D. () () () () () () () () () + NFE : + NFE : mode = FLOODING + NFE : + NFE : CV #1 + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : monitor_file = abmd.1.txt + NFE : monitor_freq = 1 (0.0020 ps) + NFE : umbrella_file = umbrella.1.nc (not found) + NFE : + NFE : umbrella discretization (new) : + NFE : CV #1 not periodic, 97 points, min/max = 0.000000/12.000000 + NFE : + NFE : flooding timescale = 1.000 ps + NFE : + NFE : () () () () () () () () () () () () () () () () () () () () () () () () + | # of SOLUTE degrees of freedom (RNDFP): 6365. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 6365. NUM_NOSHAKE = 0 CORRECTED RNDFP = 6365. @@ -188,158 +213,203 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 650835 +| Local SIZE OF NONBOND LIST = 329344 | TOTAL SIZE OF NONBOND LIST = 650835 - NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.81 PRESS = 0.0 - Etot = -8244.5620 EKtot = 1915.0482 EPtot = -10159.6103 - BOND = 20.7161 ANGLE = 61.6307 DIHED = 75.4253 - 1-4 NB = 33.3315 1-4 EEL = 538.6688 VDWAALS = 1411.5868 - EELEC = -12300.9694 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1146E-03 - TEMP0 = 310.0000 REPNUM = 1 EXCHANGE# = 1 + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 281.56 PRESS = 0.0 + Etot = -8485.5403 EKtot = 1780.6314 EPtot = -10266.1717 + BOND = 28.3262 ANGLE = 51.6386 DIHED = 71.6224 + 1-4 NB = 28.8645 1-4 EEL = 540.6128 VDWAALS = 1437.6257 + EELEC = -12424.8699 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10266.1797 + Ewald error estimate: 0.4452E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 1 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.93 PRESS = 0.0 - Etot = -8250.2509 EKtot = 1922.1055 EPtot = -10172.3563 - BOND = 29.5526 ANGLE = 71.1685 DIHED = 77.7648 - 1-4 NB = 32.9889 1-4 EEL = 534.6458 VDWAALS = 1402.7816 - EELEC = -12321.2587 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1220E-03 - TEMP0 = 310.0000 REPNUM = 1 EXCHANGE# = 2 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 282.73 PRESS = 0.0 + Etot = -8500.5684 EKtot = 1788.0399 EPtot = -10288.6084 + BOND = 22.7739 ANGLE = 77.7414 DIHED = 75.2236 + 1-4 NB = 31.1806 1-4 EEL = 514.8200 VDWAALS = 1409.3457 + EELEC = -12419.7016 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10288.6163 + Ewald error estimate: 0.3772E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 2 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 315.20 PRESS = 0.0 - Etot = -8192.6744 EKtot = 1993.4141 EPtot = -10186.0885 - BOND = 21.8500 ANGLE = 73.3062 DIHED = 73.0947 - 1-4 NB = 32.4097 1-4 EEL = 540.0898 VDWAALS = 1398.1787 - EELEC = -12325.0176 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4367E-05 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 3 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 281.87 PRESS = 0.0 + Etot = -8485.3619 EKtot = 1782.6102 EPtot = -10267.9721 + BOND = 25.6633 ANGLE = 68.9034 DIHED = 77.2181 + 1-4 NB = 32.3389 1-4 EEL = 518.7029 VDWAALS = 1411.9494 + EELEC = -12402.7661 EHBOND = 0.0000 RESTRAINT = 0.0179 + EAMBER (non-restraint) = -10267.9900 + Ewald error estimate: 0.3089E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 3 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 307.66 PRESS = 0.0 - Etot = -8197.7159 EKtot = 1945.6990 EPtot = -10143.4149 - BOND = 29.8272 ANGLE = 71.7243 DIHED = 75.8195 - 1-4 NB = 35.4000 1-4 EEL = 541.7574 VDWAALS = 1388.4329 - EELEC = -12286.3762 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.6189E-04 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 4 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 286.39 PRESS = 0.0 + Etot = -8477.4535 EKtot = 1811.1848 EPtot = -10288.6383 + BOND = 24.5019 ANGLE = 69.9706 DIHED = 70.7583 + 1-4 NB = 30.7480 1-4 EEL = 522.6108 VDWAALS = 1409.7292 + EELEC = -12416.9848 EHBOND = 0.0000 RESTRAINT = 0.0277 + EAMBER (non-restraint) = -10288.6660 + Ewald error estimate: 0.1417E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 4 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 298.35 PRESS = 0.0 - Etot = -8268.4025 EKtot = 1886.8163 EPtot = -10155.2188 - BOND = 27.2855 ANGLE = 57.8217 DIHED = 79.4308 - 1-4 NB = 33.1585 1-4 EEL = 540.6268 VDWAALS = 1389.7125 - EELEC = -12283.2545 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.6283E-04 - TEMP0 = 310.0000 REPNUM = 1 EXCHANGE# = 5 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.028 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 285.48 PRESS = 0.0 + Etot = -8464.8670 EKtot = 1805.4275 EPtot = -10270.2945 + BOND = 25.8437 ANGLE = 68.4407 DIHED = 73.3978 + 1-4 NB = 34.4474 1-4 EEL = 526.8911 VDWAALS = 1420.2640 + EELEC = -12419.6164 EHBOND = 0.0000 RESTRAINT = 0.0372 + EAMBER (non-restraint) = -10270.3317 + Ewald error estimate: 0.2211E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 5 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 299.02 PRESS = 0.0 - Etot = -8262.7482 EKtot = 1891.0753 EPtot = -10153.8236 - BOND = 32.7221 ANGLE = 60.9494 DIHED = 80.6808 - 1-4 NB = 34.8732 1-4 EEL = 538.1895 VDWAALS = 1412.3505 - EELEC = -12313.5890 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1411E-03 - TEMP0 = 310.0000 REPNUM = 1 EXCHANGE# = 6 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.037 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 278.55 PRESS = 0.0 + Etot = -8473.9889 EKtot = 1761.6080 EPtot = -10235.5969 + BOND = 25.1293 ANGLE = 54.6139 DIHED = 75.2849 + 1-4 NB = 34.5101 1-4 EEL = 534.3232 VDWAALS = 1430.1675 + EELEC = -12389.6438 EHBOND = 0.0000 RESTRAINT = 0.0179 + EAMBER (non-restraint) = -10235.6148 + Ewald error estimate: 0.3339E-05 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 6 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 299.20 PRESS = 0.0 - Etot = -8202.7759 EKtot = 1892.2311 EPtot = -10095.0070 - BOND = 29.9574 ANGLE = 62.7982 DIHED = 75.9139 - 1-4 NB = 35.7799 1-4 EEL = 541.3901 VDWAALS = 1419.1172 - EELEC = -12259.9638 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1702E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 7 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 289.15 PRESS = 0.0 + Etot = -8466.5234 EKtot = 1828.6772 EPtot = -10295.2006 + BOND = 20.2903 ANGLE = 64.2051 DIHED = 79.4738 + 1-4 NB = 33.3934 1-4 EEL = 539.3366 VDWAALS = 1423.3000 + EELEC = -12455.2276 EHBOND = 0.0000 RESTRAINT = 0.0278 + EAMBER (non-restraint) = -10295.2284 + Ewald error estimate: 0.3757E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 7 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 293.50 PRESS = 0.0 - Etot = -8202.5132 EKtot = 1856.1553 EPtot = -10058.6685 - BOND = 23.0922 ANGLE = 71.3914 DIHED = 76.2400 - 1-4 NB = 37.7572 1-4 EEL = 534.7837 VDWAALS = 1389.8401 - EELEC = -12191.7730 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2694E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 8 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.028 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 278.90 PRESS = 0.0 + Etot = -8463.2623 EKtot = 1763.8512 EPtot = -10227.1135 + BOND = 28.5550 ANGLE = 53.2424 DIHED = 79.6043 + 1-4 NB = 33.0468 1-4 EEL = 541.5730 VDWAALS = 1425.2682 + EELEC = -12388.4407 EHBOND = 0.0000 RESTRAINT = 0.0376 + EAMBER (non-restraint) = -10227.1511 + Ewald error estimate: 0.2589E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 8 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 296.71 PRESS = 0.0 - Etot = -8201.1055 EKtot = 1876.4821 EPtot = -10077.5875 - BOND = 24.9434 ANGLE = 74.7948 DIHED = 74.0980 - 1-4 NB = 37.7700 1-4 EEL = 533.9930 VDWAALS = 1348.1866 - EELEC = -12171.3733 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4199E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 9 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.038 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 284.69 PRESS = 0.0 + Etot = -8471.3877 EKtot = 1800.4281 EPtot = -10271.8157 + BOND = 27.4332 ANGLE = 54.3325 DIHED = 76.5791 + 1-4 NB = 32.5745 1-4 EEL = 544.9750 VDWAALS = 1441.0376 + EELEC = -12448.7952 EHBOND = 0.0000 RESTRAINT = 0.0475 + EAMBER (non-restraint) = -10271.8632 + Ewald error estimate: 0.1330E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 9 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 307.03 PRESS = 0.0 - Etot = -8180.8393 EKtot = 1941.7242 EPtot = -10122.5635 - BOND = 24.7927 ANGLE = 66.2840 DIHED = 72.4316 - 1-4 NB = 34.8593 1-4 EEL = 537.3850 VDWAALS = 1325.2014 - EELEC = -12183.5175 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3412E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 10 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.047 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 284.04 PRESS = 0.0 + Etot = -8454.5751 EKtot = 1796.3375 EPtot = -10250.9126 + BOND = 27.8333 ANGLE = 67.3063 DIHED = 71.5455 + 1-4 NB = 32.7790 1-4 EEL = 518.9435 VDWAALS = 1384.4627 + EELEC = -12353.8244 EHBOND = 0.0000 RESTRAINT = 0.0414 + EAMBER (non-restraint) = -10250.9540 + Ewald error estimate: 0.1340E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 10 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.041 + BBMD : 0.000 STSM : 0.000 +=============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.27% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.26% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.29 (89.86% of List ) -| Other 0.03 (10.14% of List ) -| List time 0.32 ( 9.68% of Nonbo) -| Short_ene time 2.28 (99.14% of Direc) -| Other 0.02 ( 0.86% of Direc) -| Direct Ewald time 2.30 (76.63% of Ewald) -| Adjust Ewald time 0.02 ( 0.62% of Ewald) +| Build the list 0.43 (95.15% of List ) +| Other 0.02 ( 4.85% of List ) +| List time 0.45 (21.91% of Nonbo) +| Short_ene time 1.08 (97.88% of Direc) +| Other 0.02 ( 2.12% of Direc) +| Direct Ewald time 1.10 (68.74% of Ewald) +| Adjust Ewald time 0.01 ( 0.49% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.03 ( 4.13% of Recip) -| Fill charge grid 0.05 ( 7.40% of Recip) -| Scalar sum 0.28 (40.99% of Recip) -| Grad sum 0.11 (16.18% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.21 (100.0% of FFT t) -| FFT time 0.21 (31.27% of Recip) -| Other 0.00 ( 0.04% of Recip) -| Recip Ewald time 0.68 (22.59% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.05% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 3.00 (90.32% of Nonbo) -| Nonbond force 3.32 (85.39% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.41% of Force) -| Other 0.55 (14.20% of Force) -| Force time 3.88 (97.09% of Runmd) -| Shake time 0.02 ( 0.42% of Runmd) -| Verlet update time 0.09 ( 2.24% of Runmd) -| Other 0.01 ( 0.26% of Runmd) -| Runmd Time 4.00 (98.50% of Total) -| Other 0.05 ( 1.21% of Total) -| Total time 4.06 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Fill Bspline coeffs 0.03 ( 6.65% of Recip) +| Fill charge grid 0.03 ( 6.81% of Recip) +| Scalar sum 0.11 (25.79% of Recip) +| Grad sum 0.07 (15.43% of Recip) +| FFT back comm time 0.01 ( 6.96% of FFT t) +| Other 0.18 (93.04% of FFT t) +| FFT time 0.20 (44.15% of Recip) +| Other 0.01 ( 1.17% of Recip) +| Recip Ewald time 0.44 (27.81% of Ewald) +| Force Adjust 0.04 ( 2.76% of Ewald) +| Virial junk 0.00 ( 0.13% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.60 (78.09% of Nonbo) +| Nonbond force 2.05 (97.05% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.38% of Force) +| FRC Collect time 0.00 ( 0.13% of Force) +| Other 0.05 ( 2.44% of Force) +| Force time 2.11 (95.37% of Runmd) +| Shake time 0.01 ( 0.23% of Runmd) +| Verlet update time 0.07 ( 3.18% of Runmd) +| CRD distribute time 0.00 ( 0.04% of Runmd) +| Other 0.03 ( 1.18% of Runmd) +| Runmd Time 2.21 (97.18% of Total) +| Other 0.06 ( 2.55% of Total) +| Total time 2.28 (100.0% of ALL ) + +| Number of list builds : 17 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 4.00 Per Step(ms) = 80.03 -| ns/day = 2.16 seconds/ns = 40014.32 +| Elapsed(s) = 2.21 Per Step(ms) = 44.27 +| ns/day = 3.90 seconds/ns = 22133.58 | ----------------------------------------------------- -| Job began at 18:10:29.129 on 06/14/2016 -| Setup done at 18:10:29.191 on 06/14/2016 -| Run done at 18:10:33.192 on 06/14/2016 -| wallclock() was called 3211 times +| Job began at 19:19:01.412 on 09/21/2018 +| Setup done at 19:19:01.477 on 09/21/2018 +| Run done at 19:19:03.690 on 09/21/2018 +| wallclock() was called 3775 times diff --git test/nfe/abremd/save/mdout.2 test/nfe/abremd/save/mdout.2 index 56e26cadba..a0dc9315bf 100644 --- test/nfe/abremd/save/mdout.2 +++ test/nfe/abremd/save/mdout.2 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/14/2016 at 18:10:29 +| Run on 09/21/2018 at 19:19:01 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/abremd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abremd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -45,8 +45,8 @@ File Assignments: ntb = 1, ntp = 0, temp0 = 310.0, ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, - ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, numexchg = 10 / @@ -90,8 +90,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -113,7 +113,7 @@ General flags: imin = 0, nmropt = 0 Replica exchange - numexchg= 10, rem= 1 + numexchg= 10, rem= 3 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 @@ -165,18 +165,43 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- + + NFE : () () () () () () () () () () A. B. M. D. () () () () () () () () () + NFE : + NFE : mode = FLOODING + NFE : + NFE : CV #1 + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : monitor_file = abmd.2.txt + NFE : monitor_freq = 2 (0.0040 ps) + NFE : umbrella_file = umbrella.2.nc (not found) + NFE : + NFE : umbrella discretization (new) : + NFE : CV #1 not periodic, 97 points, min/max = 0.000000/12.000000 + NFE : + NFE : flooding timescale = 2.000 ps + NFE : + NFE : () () () () () () () () () () () () () () () () () () () () () () () () + | # of SOLUTE degrees of freedom (RNDFP): 6365. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 6365. NUM_NOSHAKE = 0 CORRECTED RNDFP = 6365. @@ -188,158 +213,203 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 651699 +| Local SIZE OF NONBOND LIST = 330734 | TOTAL SIZE OF NONBOND LIST = 651699 - NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 295.85 PRESS = 0.0 - Etot = -8443.9016 EKtot = 1871.0490 EPtot = -10314.9506 - BOND = 28.7910 ANGLE = 68.1473 DIHED = 69.9813 - 1-4 NB = 30.9578 1-4 EEL = 509.2244 VDWAALS = 1396.6115 - EELEC = -12418.6640 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4604E-03 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 1 + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 296.01 PRESS = 0.0 + Etot = -8442.7202 EKtot = 1872.0385 EPtot = -10314.7587 + BOND = 28.7973 ANGLE = 68.1657 DIHED = 69.9843 + 1-4 NB = 30.9606 1-4 EEL = 509.2245 VDWAALS = 1396.6565 + EELEC = -12418.5516 EHBOND = 0.0000 RESTRAINT = 0.0040 + EAMBER (non-restraint) = -10314.7627 + Ewald error estimate: 0.4603E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 1 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 289.48 PRESS = 0.0 - Etot = -8446.2663 EKtot = 1830.7303 EPtot = -10276.9966 - BOND = 23.4977 ANGLE = 78.4175 DIHED = 75.4348 - 1-4 NB = 31.3151 1-4 EEL = 514.7663 VDWAALS = 1411.0023 - EELEC = -12411.4301 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4098E-03 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 2 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.004 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 286.07 PRESS = 0.0 + Etot = -8428.4784 EKtot = 1809.1959 EPtot = -10237.6742 + BOND = 28.4849 ANGLE = 65.6221 DIHED = 84.4329 + 1-4 NB = 29.7197 1-4 EEL = 535.1655 VDWAALS = 1433.8230 + EELEC = -12414.9262 EHBOND = 0.0000 RESTRAINT = 0.0040 + EAMBER (non-restraint) = -10237.6782 + Ewald error estimate: 0.3550E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 2 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 284.89 PRESS = 0.0 - Etot = -8441.1030 EKtot = 1801.7103 EPtot = -10242.8133 - BOND = 26.2834 ANGLE = 69.3370 DIHED = 77.6455 - 1-4 NB = 32.3026 1-4 EEL = 519.1941 VDWAALS = 1420.3201 - EELEC = -12387.8960 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3651E-03 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 3 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.004 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 280.35 PRESS = 0.0 + Etot = -8423.9007 EKtot = 1772.9960 EPtot = -10196.8967 + BOND = 30.2828 ANGLE = 61.6855 DIHED = 83.3316 + 1-4 NB = 28.8639 1-4 EEL = 528.6148 VDWAALS = 1444.2095 + EELEC = -12373.8936 EHBOND = 0.0000 RESTRAINT = 0.0090 + EAMBER (non-restraint) = -10196.9057 + Ewald error estimate: 0.2608E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 3 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 290.14 PRESS = 0.0 - Etot = -8443.6864 EKtot = 1834.9005 EPtot = -10278.5869 - BOND = 23.6912 ANGLE = 70.6181 DIHED = 72.3665 - 1-4 NB = 30.1036 1-4 EEL = 524.3013 VDWAALS = 1419.7880 - EELEC = -12419.4558 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3722E-03 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 4 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.009 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 282.08 PRESS = 0.0 + Etot = -8410.5818 EKtot = 1783.9134 EPtot = -10194.4952 + BOND = 33.4399 ANGLE = 67.3821 DIHED = 78.0307 + 1-4 NB = 30.6469 1-4 EEL = 537.9276 VDWAALS = 1439.9106 + EELEC = -12381.8470 EHBOND = 0.0000 RESTRAINT = 0.0139 + EAMBER (non-restraint) = -10194.5091 + Ewald error estimate: 0.2484E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 4 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 288.76 PRESS = 0.0 - Etot = -8448.0660 EKtot = 1826.1678 EPtot = -10274.2338 - BOND = 25.6238 ANGLE = 66.3859 DIHED = 73.4991 - 1-4 NB = 33.2964 1-4 EEL = 527.0465 VDWAALS = 1431.1536 - EELEC = -12431.2390 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2107E-03 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 5 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.014 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 288.73 PRESS = 0.0 + Etot = -8417.6120 EKtot = 1825.9965 EPtot = -10243.6085 + BOND = 24.3034 ANGLE = 56.7175 DIHED = 83.0985 + 1-4 NB = 32.6221 1-4 EEL = 537.5005 VDWAALS = 1438.1636 + EELEC = -12416.0330 EHBOND = 0.0000 RESTRAINT = 0.0189 + EAMBER (non-restraint) = -10243.6274 + Ewald error estimate: 0.7670E-04 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 5 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 285.36 PRESS = 0.0 - Etot = -8433.7308 EKtot = 1804.7149 EPtot = -10238.4457 - BOND = 20.0724 ANGLE = 76.2218 DIHED = 68.9045 - 1-4 NB = 31.7704 1-4 EEL = 523.8580 VDWAALS = 1446.0189 - EELEC = -12405.2918 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1992E-05 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 6 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.019 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 290.19 PRESS = 0.0 + Etot = -8390.9629 EKtot = 1835.2412 EPtot = -10226.2041 + BOND = 20.1724 ANGLE = 75.7803 DIHED = 70.8407 + 1-4 NB = 32.2808 1-4 EEL = 524.3381 VDWAALS = 1436.4806 + EELEC = -12386.1055 EHBOND = 0.0000 RESTRAINT = 0.0085 + EAMBER (non-restraint) = -10226.2126 + Ewald error estimate: 0.1531E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 6 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 285.62 PRESS = 0.0 - Etot = -8419.0053 EKtot = 1806.3282 EPtot = -10225.3335 - BOND = 22.6102 ANGLE = 62.4916 DIHED = 76.5653 - 1-4 NB = 31.2856 1-4 EEL = 524.6937 VDWAALS = 1438.5631 - EELEC = -12381.5431 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5491E-05 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 7 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 289.29 PRESS = 0.0 + Etot = -8382.6432 EKtot = 1829.5160 EPtot = -10212.1592 + BOND = 21.4426 ANGLE = 61.6042 DIHED = 78.3466 + 1-4 NB = 31.2549 1-4 EEL = 525.8437 VDWAALS = 1431.8360 + EELEC = -12362.5003 EHBOND = 0.0000 RESTRAINT = 0.0131 + EAMBER (non-restraint) = -10212.1723 + Ewald error estimate: 0.1249E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 7 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 295.09 PRESS = 0.0 - Etot = -8363.9435 EKtot = 1866.1946 EPtot = -10230.1380 - BOND = 30.9849 ANGLE = 69.9658 DIHED = 75.4731 - 1-4 NB = 29.2988 1-4 EEL = 525.6980 VDWAALS = 1425.2384 - EELEC = -12386.7971 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3223E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.013 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 292.05 PRESS = 0.0 + Etot = -8388.0483 EKtot = 1846.9753 EPtot = -10235.0236 + BOND = 28.3124 ANGLE = 68.7035 DIHED = 77.2483 + 1-4 NB = 29.1650 1-4 EEL = 524.7526 VDWAALS = 1417.4880 + EELEC = -12380.7112 EHBOND = 0.0000 RESTRAINT = 0.0178 + EAMBER (non-restraint) = -10235.0413 + Ewald error estimate: 0.2977E-03 TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 8 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 287.97 PRESS = 0.0 - Etot = -8372.4618 EKtot = 1821.2210 EPtot = -10193.6827 - BOND = 27.2785 ANGLE = 77.7902 DIHED = 70.6313 - 1-4 NB = 31.4513 1-4 EEL = 521.2168 VDWAALS = 1412.2394 - EELEC = -12334.2903 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1744E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 287.83 PRESS = 0.0 + Etot = -8395.2054 EKtot = 1820.3134 EPtot = -10215.5188 + BOND = 25.2842 ANGLE = 73.3605 DIHED = 70.6626 + 1-4 NB = 31.5238 1-4 EEL = 518.2659 VDWAALS = 1398.0348 + EELEC = -12332.6731 EHBOND = 0.0000 RESTRAINT = 0.0225 + EAMBER (non-restraint) = -10215.5413 + Ewald error estimate: 0.1576E-03 TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 9 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 293.03 PRESS = 0.0 - Etot = -8372.1176 EKtot = 1853.2188 EPtot = -10225.3364 - BOND = 26.0680 ANGLE = 69.4187 DIHED = 72.2105 - 1-4 NB = 32.7397 1-4 EEL = 522.8478 VDWAALS = 1400.0150 - EELEC = -12348.6361 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4304E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.023 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 282.50 PRESS = 0.0 + Etot = -8399.9889 EKtot = 1786.6256 EPtot = -10186.6145 + BOND = 33.6037 ANGLE = 60.0991 DIHED = 78.8605 + 1-4 NB = 34.6313 1-4 EEL = 542.7805 VDWAALS = 1481.7791 + EELEC = -12418.3923 EHBOND = 0.0000 RESTRAINT = 0.0236 + EAMBER (non-restraint) = -10186.6381 + Ewald error estimate: 0.2541E-03 TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 10 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.024 + BBMD : 0.000 STSM : 0.000 +=============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.27% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.26% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.29 (90.80% of List ) -| Other 0.03 ( 9.20% of List ) -| List time 0.32 ( 9.51% of Nonbo) -| Short_ene time 2.30 (99.12% of Direc) -| Other 0.02 ( 0.88% of Direc) -| Direct Ewald time 2.32 (76.86% of Ewald) -| Adjust Ewald time 0.02 ( 0.62% of Ewald) +| Build the list 0.46 (95.47% of List ) +| Other 0.02 ( 4.53% of List ) +| List time 0.48 (23.13% of Nonbo) +| Short_ene time 1.13 (97.80% of Direc) +| Other 0.03 ( 2.20% of Direc) +| Direct Ewald time 1.15 (71.80% of Ewald) +| Adjust Ewald time 0.01 ( 0.52% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.03 ( 4.21% of Recip) -| Fill charge grid 0.05 ( 7.59% of Recip) -| Scalar sum 0.28 (40.78% of Recip) -| Grad sum 0.11 (16.16% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.21 (100.0% of FFT t) -| FFT time 0.21 (31.23% of Recip) -| Other 0.00 ( 0.04% of Recip) -| Recip Ewald time 0.67 (22.38% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.04% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 3.02 (90.48% of Nonbo) -| Nonbond force 3.33 (85.74% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.41% of Force) -| Other 0.54 (13.85% of Force) -| Force time 3.89 (97.14% of Runmd) -| Shake time 0.02 ( 0.42% of Runmd) -| Verlet update time 0.09 ( 2.20% of Runmd) -| Other 0.01 ( 0.25% of Runmd) -| Runmd Time 4.00 (98.49% of Total) -| Other 0.05 ( 1.23% of Total) -| Total time 4.06 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Fill Bspline coeffs 0.03 ( 6.76% of Recip) +| Fill charge grid 0.03 ( 7.57% of Recip) +| Scalar sum 0.12 (28.29% of Recip) +| Grad sum 0.07 (17.25% of Recip) +| FFT back comm time 0.01 ( 7.93% of FFT t) +| Other 0.15 (92.07% of FFT t) +| FFT time 0.17 (39.80% of Recip) +| Other 0.00 ( 0.32% of Recip) +| Recip Ewald time 0.42 (26.24% of Ewald) +| Force Adjust 0.02 ( 1.24% of Ewald) +| Virial junk 0.00 ( 0.13% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.61 (76.86% of Nonbo) +| Nonbond force 2.09 (98.55% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.39% of Force) +| FRC Collect time 0.00 ( 0.13% of Force) +| Other 0.02 ( 0.93% of Force) +| Force time 2.12 (95.73% of Runmd) +| Shake time 0.01 ( 0.24% of Runmd) +| Verlet update time 0.07 ( 3.19% of Runmd) +| CRD distribute time 0.00 ( 0.03% of Runmd) +| Other 0.02 ( 0.81% of Runmd) +| Runmd Time 2.21 (97.18% of Total) +| Other 0.06 ( 2.55% of Total) +| Total time 2.28 (100.0% of ALL ) + +| Number of list builds : 18 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 4.00 Per Step(ms) = 80.03 -| ns/day = 2.16 seconds/ns = 40014.42 +| Elapsed(s) = 2.22 Per Step(ms) = 44.31 +| ns/day = 3.90 seconds/ns = 22153.13 | ----------------------------------------------------- -| Job began at 18:10:29.129 on 06/14/2016 -| Setup done at 18:10:29.191 on 06/14/2016 -| Run done at 18:10:33.192 on 06/14/2016 -| wallclock() was called 3211 times +| Job began at 19:19:01.412 on 09/21/2018 +| Setup done at 19:19:01.477 on 09/21/2018 +| Run done at 19:19:03.692 on 09/21/2018 +| wallclock() was called 3777 times diff --git test/nfe/abremd/save/mdout.3 test/nfe/abremd/save/mdout.3 index 1706d754d5..a1bd1b498e 100644 --- test/nfe/abremd/save/mdout.3 +++ test/nfe/abremd/save/mdout.3 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/14/2016 at 18:10:29 +| Run on 09/21/2018 at 19:19:01 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/abremd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abremd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -45,8 +45,8 @@ File Assignments: ntb = 1, ntp = 0, temp0 = 320.0, ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, - ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, numexchg = 10 / @@ -90,8 +90,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -113,7 +113,7 @@ General flags: imin = 0, nmropt = 0 Replica exchange - numexchg= 10, rem= 1 + numexchg= 10, rem= 3 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 @@ -165,18 +165,43 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- + + NFE : () () () () () () () () () () A. B. M. D. () () () () () () () () () + NFE : + NFE : mode = FLOODING + NFE : + NFE : CV #1 + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : monitor_file = abmd.3.txt + NFE : monitor_freq = 3 (0.0060 ps) + NFE : umbrella_file = umbrella.3.nc (not found) + NFE : + NFE : umbrella discretization (new) : + NFE : CV #1 not periodic, 97 points, min/max = 0.000000/12.000000 + NFE : + NFE : flooding timescale = 4.000 ps + NFE : + NFE : () () () () () () () () () () () () () () () () () () () () () () () () + | # of SOLUTE degrees of freedom (RNDFP): 6365. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 6365. NUM_NOSHAKE = 0 CORRECTED RNDFP = 6365. @@ -188,158 +213,203 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 650919 +| Local SIZE OF NONBOND LIST = 328843 | TOTAL SIZE OF NONBOND LIST = 650919 - NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 310.03 PRESS = 0.0 - Etot = -8147.3370 EKtot = 1960.7134 EPtot = -10108.0503 - BOND = 28.5942 ANGLE = 66.3317 DIHED = 73.9462 - 1-4 NB = 29.5040 1-4 EEL = 526.9495 VDWAALS = 1332.3900 - EELEC = -12165.7659 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1868E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 1 + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 309.88 PRESS = 0.0 + Etot = -8148.4280 EKtot = 1959.7460 EPtot = -10108.1740 + BOND = 28.5765 ANGLE = 66.3283 DIHED = 73.9458 + 1-4 NB = 29.5050 1-4 EEL = 526.9483 VDWAALS = 1332.3812 + EELEC = -12165.8610 EHBOND = 0.0000 RESTRAINT = 0.0020 + EAMBER (non-restraint) = -10108.1760 + Ewald error estimate: 0.1892E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 1 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 304.61 PRESS = 0.0 - Etot = -8138.7025 EKtot = 1926.3968 EPtot = -10065.0992 - BOND = 34.5145 ANGLE = 59.0620 DIHED = 76.2926 - 1-4 NB = 30.9071 1-4 EEL = 526.0751 VDWAALS = 1336.4496 - EELEC = -12128.4001 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.7804E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 2 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.002 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 318.79 PRESS = 0.0 + Etot = -8058.6959 EKtot = 2016.1166 EPtot = -10074.8125 + BOND = 33.1863 ANGLE = 71.4355 DIHED = 79.8458 + 1-4 NB = 33.5736 1-4 EEL = 534.0249 VDWAALS = 1428.4767 + EELEC = -12255.3573 EHBOND = 0.0000 RESTRAINT = 0.0020 + EAMBER (non-restraint) = -10074.8145 + Ewald error estimate: 0.8594E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 2 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 311.68 PRESS = 0.0 - Etot = -8123.4201 EKtot = 1971.1658 EPtot = -10094.5859 - BOND = 35.4631 ANGLE = 57.8470 DIHED = 76.1443 - 1-4 NB = 29.2665 1-4 EEL = 521.8588 VDWAALS = 1326.8648 - EELEC = -12142.0304 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1314E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 3 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.002 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 324.59 PRESS = 0.0 + Etot = -8058.1295 EKtot = 2052.7870 EPtot = -10110.9165 + BOND = 24.5371 ANGLE = 73.3636 DIHED = 73.8941 + 1-4 NB = 32.7485 1-4 EEL = 541.6067 VDWAALS = 1431.8270 + EELEC = -12288.8979 EHBOND = 0.0000 RESTRAINT = 0.0045 + EAMBER (non-restraint) = -10110.9209 + Ewald error estimate: 0.5370E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 3 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 307.52 PRESS = 0.0 - Etot = -8108.7452 EKtot = 1944.8385 EPtot = -10053.5837 - BOND = 27.3650 ANGLE = 63.3337 DIHED = 77.0534 - 1-4 NB = 32.0497 1-4 EEL = 522.3056 VDWAALS = 1308.2066 - EELEC = -12083.8976 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.6501E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 4 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.004 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 321.25 PRESS = 0.0 + Etot = -8043.2862 EKtot = 2031.6912 EPtot = -10074.9773 + BOND = 31.7722 ANGLE = 75.1007 DIHED = 78.2022 + 1-4 NB = 36.1720 1-4 EEL = 543.1065 VDWAALS = 1417.2884 + EELEC = -12256.6262 EHBOND = 0.0000 RESTRAINT = 0.0070 + EAMBER (non-restraint) = -10074.9843 + Ewald error estimate: 0.3465E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 4 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 315.05 PRESS = 0.0 - Etot = -8095.0649 EKtot = 1992.4535 EPtot = -10087.5183 - BOND = 22.3806 ANGLE = 69.4307 DIHED = 73.2854 - 1-4 NB = 30.2758 1-4 EEL = 524.9455 VDWAALS = 1295.2646 - EELEC = -12103.1010 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1601E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 5 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.007 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 317.84 PRESS = 0.0 + Etot = -8049.6241 EKtot = 2010.1250 EPtot = -10059.7491 + BOND = 31.8399 ANGLE = 61.3675 DIHED = 82.6976 + 1-4 NB = 33.4875 1-4 EEL = 541.5647 VDWAALS = 1413.3763 + EELEC = -12224.0919 EHBOND = 0.0000 RESTRAINT = 0.0094 + EAMBER (non-restraint) = -10059.7585 + Ewald error estimate: 0.3124E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 5 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 312.48 PRESS = 0.0 - Etot = -8094.1814 EKtot = 1976.2016 EPtot = -10070.3830 - BOND = 36.7981 ANGLE = 66.7393 DIHED = 75.9361 - 1-4 NB = 30.7857 1-4 EEL = 515.2861 VDWAALS = 1287.7564 - EELEC = -12083.6848 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1219E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 6 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.009 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 306.46 PRESS = 0.0 + Etot = -8136.8323 EKtot = 1938.0956 EPtot = -10074.9279 + BOND = 34.4843 ANGLE = 65.1103 DIHED = 74.6808 + 1-4 NB = 31.1545 1-4 EEL = 515.1708 VDWAALS = 1290.7523 + EELEC = -12086.2850 EHBOND = 0.0000 RESTRAINT = 0.0041 + EAMBER (non-restraint) = -10074.9320 + Ewald error estimate: 0.3167E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 6 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 310.75 PRESS = 0.0 - Etot = -8095.2337 EKtot = 1965.2562 EPtot = -10060.4900 - BOND = 20.0904 ANGLE = 60.1119 DIHED = 78.5681 - 1-4 NB = 30.5772 1-4 EEL = 534.1233 VDWAALS = 1282.8654 - EELEC = -12066.8263 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1370E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 7 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.004 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 310.06 PRESS = 0.0 + Etot = -8136.6527 EKtot = 1960.9141 EPtot = -10097.5669 + BOND = 18.2606 ANGLE = 58.2778 DIHED = 78.5227 + 1-4 NB = 30.4289 1-4 EEL = 534.5776 VDWAALS = 1278.1400 + EELEC = -12095.7810 EHBOND = 0.0000 RESTRAINT = 0.0064 + EAMBER (non-restraint) = -10097.5733 + Ewald error estimate: 0.2049E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 7 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 313.49 PRESS = 0.0 - Etot = -8088.7439 EKtot = 1982.6049 EPtot = -10071.3488 - BOND = 25.3089 ANGLE = 61.0926 DIHED = 76.3594 - 1-4 NB = 31.6360 1-4 EEL = 533.1503 VDWAALS = 1287.5327 - EELEC = -12086.4287 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5848E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 8 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.006 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 306.07 PRESS = 0.0 + Etot = -8132.1078 EKtot = 1935.6322 EPtot = -10067.7400 + BOND = 22.7527 ANGLE = 60.6713 DIHED = 76.6262 + 1-4 NB = 32.0402 1-4 EEL = 533.5929 VDWAALS = 1287.2367 + EELEC = -12080.6689 EHBOND = 0.0000 RESTRAINT = 0.0088 + EAMBER (non-restraint) = -10067.7489 + Ewald error estimate: 0.1371E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 8 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 313.18 PRESS = 0.0 - Etot = -8089.6193 EKtot = 1980.6256 EPtot = -10070.2449 - BOND = 33.9006 ANGLE = 73.5083 DIHED = 70.4670 - 1-4 NB = 29.4744 1-4 EEL = 527.3568 VDWAALS = 1306.0687 - EELEC = -12111.0207 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3901E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 9 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.009 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 307.79 PRESS = 0.0 + Etot = -8130.1903 EKtot = 1946.5193 EPtot = -10076.7096 + BOND = 30.2595 ANGLE = 68.2161 DIHED = 70.8370 + 1-4 NB = 29.3837 1-4 EEL = 529.2474 VDWAALS = 1309.3363 + EELEC = -12114.0008 EHBOND = 0.0000 RESTRAINT = 0.0111 + EAMBER (non-restraint) = -10076.7207 + Ewald error estimate: 0.1146E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 9 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 310.87 PRESS = 0.0 - Etot = -8089.4424 EKtot = 1966.0348 EPtot = -10055.4771 - BOND = 30.8418 ANGLE = 66.2822 DIHED = 74.9671 - 1-4 NB = 32.4854 1-4 EEL = 541.3523 VDWAALS = 1341.0855 - EELEC = -12142.4914 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2932E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 10 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.011 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 307.27 PRESS = 0.0 + Etot = -8130.2838 EKtot = 1943.2769 EPtot = -10073.5608 + BOND = 27.5660 ANGLE = 62.2577 DIHED = 74.7710 + 1-4 NB = 33.7953 1-4 EEL = 542.2517 VDWAALS = 1336.2511 + EELEC = -12150.4671 EHBOND = 0.0000 RESTRAINT = 0.0136 + EAMBER (non-restraint) = -10073.5743 + Ewald error estimate: 0.8009E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 10 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.014 + BBMD : 0.000 STSM : 0.000 +=============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.28% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.26% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.29 (90.80% of List ) -| Other 0.03 ( 9.20% of List ) -| List time 0.32 ( 9.49% of Nonbo) -| Short_ene time 2.29 (99.14% of Direc) -| Other 0.02 ( 0.86% of Direc) -| Direct Ewald time 2.31 (76.84% of Ewald) -| Adjust Ewald time 0.02 ( 0.61% of Ewald) +| Build the list 0.49 (95.74% of List ) +| Other 0.02 ( 4.26% of List ) +| List time 0.51 (24.27% of Nonbo) +| Short_ene time 1.13 (97.86% of Direc) +| Other 0.02 ( 2.14% of Direc) +| Direct Ewald time 1.16 (72.61% of Ewald) +| Adjust Ewald time 0.01 ( 0.51% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.03 ( 4.15% of Recip) -| Fill charge grid 0.05 ( 7.49% of Recip) -| Scalar sum 0.28 (40.95% of Recip) -| Grad sum 0.11 (16.19% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.21 (100.0% of FFT t) -| FFT time 0.21 (31.18% of Recip) -| Other 0.00 ( 0.04% of Recip) -| Recip Ewald time 0.67 (22.41% of Ewald) -| Force Adjust 0.00 ( 0.02% of Ewald) -| Virial junk 0.00 ( 0.04% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 3.01 (90.51% of Nonbo) -| Nonbond force 3.32 (85.52% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.40% of Force) -| Other 0.55 (14.08% of Force) -| Force time 3.88 (97.10% of Runmd) -| Shake time 0.02 ( 0.42% of Runmd) -| Verlet update time 0.09 ( 2.19% of Runmd) -| Other 0.01 ( 0.29% of Runmd) -| Runmd Time 4.00 (98.48% of Total) -| Other 0.05 ( 1.24% of Total) -| Total time 4.06 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Fill Bspline coeffs 0.03 ( 6.87% of Recip) +| Fill charge grid 0.03 ( 7.82% of Recip) +| Scalar sum 0.12 (29.48% of Recip) +| Grad sum 0.07 (17.77% of Recip) +| FFT back comm time 0.01 ( 8.65% of FFT t) +| Other 0.14 (91.35% of FFT t) +| FFT time 0.15 (37.76% of Recip) +| Other 0.00 ( 0.30% of Recip) +| Recip Ewald time 0.41 (25.50% of Ewald) +| Force Adjust 0.02 ( 1.16% of Ewald) +| Virial junk 0.00 ( 0.14% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.59 (75.73% of Nonbo) +| Nonbond force 2.11 (99.22% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.39% of Force) +| FRC Collect time 0.00 ( 0.13% of Force) +| Other 0.01 ( 0.26% of Force) +| Force time 2.12 (95.75% of Runmd) +| Shake time 0.01 ( 0.24% of Runmd) +| Verlet update time 0.07 ( 3.19% of Runmd) +| CRD distribute time 0.00 ( 0.04% of Runmd) +| Other 0.02 ( 0.79% of Runmd) +| Runmd Time 2.22 (97.18% of Total) +| Other 0.06 ( 2.55% of Total) +| Total time 2.28 (100.0% of ALL ) + +| Number of list builds : 19 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 4.00 Per Step(ms) = 80.02 -| ns/day = 2.16 seconds/ns = 40010.19 +| Elapsed(s) = 2.22 Per Step(ms) = 44.33 +| ns/day = 3.90 seconds/ns = 22163.06 | ----------------------------------------------------- -| Job began at 18:10:29.129 on 06/14/2016 -| Setup done at 18:10:29.192 on 06/14/2016 -| Run done at 18:10:33.192 on 06/14/2016 -| wallclock() was called 3211 times +| Job began at 19:19:01.412 on 09/21/2018 +| Setup done at 19:19:01.477 on 09/21/2018 +| Run done at 19:19:03.693 on 09/21/2018 +| wallclock() was called 3779 times diff --git test/nfe/abremd/save/mdout.4 test/nfe/abremd/save/mdout.4 index a9e815cd7a..c4ee6e1859 100644 --- test/nfe/abremd/save/mdout.4 +++ test/nfe/abremd/save/mdout.4 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/14/2016 at 18:10:29 +| Run on 09/21/2018 at 19:19:01 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/abremd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/abremd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -45,8 +45,8 @@ File Assignments: ntb = 1, ntp = 0, temp0 = 330.0, ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, - ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, infe = 1, numexchg = 10 / @@ -90,8 +90,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -113,7 +113,7 @@ General flags: imin = 0, nmropt = 0 Replica exchange - numexchg= 10, rem= 1 + numexchg= 10, rem= 3 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 @@ -165,18 +165,43 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- + + NFE : () () () () () () () () () () A. B. M. D. () () () () () () () () () + NFE : + NFE : mode = FLOODING + NFE : + NFE : CV #1 + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : monitor_file = abmd.4.txt + NFE : monitor_freq = 5 (0.0100 ps) + NFE : umbrella_file = umbrella.4.nc (not found) + NFE : + NFE : umbrella discretization (new) : + NFE : CV #1 not periodic, 97 points, min/max = 0.000000/12.000000 + NFE : + NFE : flooding timescale = 1.000 ps + NFE : + NFE : () () () () () () () () () () () () () () () () () () () () () () () () + | # of SOLUTE degrees of freedom (RNDFP): 6365. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 6365. NUM_NOSHAKE = 0 CORRECTED RNDFP = 6365. @@ -188,158 +213,203 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 651355 +| Local SIZE OF NONBOND LIST = 321415 | TOTAL SIZE OF NONBOND LIST = 651355 - NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 309.86 PRESS = 0.0 - Etot = -8241.0911 EKtot = 1959.6162 EPtot = -10200.7073 - BOND = 30.2004 ANGLE = 55.1570 DIHED = 72.4475 - 1-4 NB = 28.5468 1-4 EEL = 540.6435 VDWAALS = 1444.4615 - EELEC = -12372.1640 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5011E-03 - TEMP0 = 320.0000 REPNUM = 4 EXCHANGE# = 1 + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 329.71 PRESS = 0.0 + Etot = -7998.9487 EKtot = 2085.1752 EPtot = -10084.1239 + BOND = 22.6133 ANGLE = 66.3319 DIHED = 76.2142 + 1-4 NB = 33.3360 1-4 EEL = 538.5129 VDWAALS = 1420.1963 + EELEC = -12241.3364 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10084.1319 + Ewald error estimate: 0.9435E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 1 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 301.97 PRESS = 0.0 - Etot = -8232.0037 EKtot = 1909.7526 EPtot = -10141.7562 - BOND = 28.7180 ANGLE = 67.3280 DIHED = 84.9041 - 1-4 NB = 29.9350 1-4 EEL = 535.6452 VDWAALS = 1463.6491 - EELEC = -12351.9356 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3104E-03 - TEMP0 = 320.0000 REPNUM = 4 EXCHANGE# = 2 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 310.83 PRESS = 0.0 + Etot = -8085.8289 EKtot = 1965.7838 EPtot = -10051.6127 + BOND = 34.5544 ANGLE = 60.0475 DIHED = 76.6088 + 1-4 NB = 30.9082 1-4 EEL = 526.4871 VDWAALS = 1341.2369 + EELEC = -12121.4636 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10051.6207 + Ewald error estimate: 0.9334E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 2 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 291.69 PRESS = 0.0 - Etot = -8286.6765 EKtot = 1844.7004 EPtot = -10131.3770 - BOND = 29.8565 ANGLE = 62.8612 DIHED = 82.1386 - 1-4 NB = 29.2321 1-4 EEL = 529.9263 VDWAALS = 1486.9381 - EELEC = -12352.3296 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1852E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 3 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 315.65 PRESS = 0.0 + Etot = -8067.8437 EKtot = 1996.2699 EPtot = -10064.1136 + BOND = 36.0130 ANGLE = 55.6940 DIHED = 77.3167 + 1-4 NB = 29.7730 1-4 EEL = 521.2952 VDWAALS = 1336.9267 + EELEC = -12121.1498 EHBOND = 0.0000 RESTRAINT = 0.0177 + EAMBER (non-restraint) = -10064.1313 + Ewald error estimate: 0.1166E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 3 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 294.60 PRESS = 0.0 - Etot = -8281.8891 EKtot = 1863.1131 EPtot = -10145.0022 - BOND = 35.5029 ANGLE = 68.1654 DIHED = 78.5848 - 1-4 NB = 30.9642 1-4 EEL = 537.4384 VDWAALS = 1479.7780 - EELEC = -12375.4359 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1694E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 4 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 312.60 PRESS = 0.0 + Etot = -8063.9959 EKtot = 1976.9515 EPtot = -10040.9474 + BOND = 27.2003 ANGLE = 62.6684 DIHED = 78.5402 + 1-4 NB = 32.1307 1-4 EEL = 522.5826 VDWAALS = 1319.6565 + EELEC = -12083.7532 EHBOND = 0.0000 RESTRAINT = 0.0272 + EAMBER (non-restraint) = -10040.9746 + Ewald error estimate: 0.1116E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 4 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 305.84 PRESS = 0.0 - Etot = -8222.9925 EKtot = 1934.1980 EPtot = -10157.1904 - BOND = 26.7730 ANGLE = 56.4161 DIHED = 82.2033 - 1-4 NB = 32.5510 1-4 EEL = 537.4124 VDWAALS = 1472.6269 - EELEC = -12365.1732 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3339E-04 - TEMP0 = 320.0000 REPNUM = 4 EXCHANGE# = 5 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.027 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 314.42 PRESS = 0.0 + Etot = -8078.5126 EKtot = 1988.4977 EPtot = -10067.0102 + BOND = 23.1027 ANGLE = 67.4259 DIHED = 72.7501 + 1-4 NB = 30.3897 1-4 EEL = 523.6899 VDWAALS = 1306.9268 + EELEC = -12091.3320 EHBOND = 0.0000 RESTRAINT = 0.0367 + EAMBER (non-restraint) = -10067.0469 + Ewald error estimate: 0.7390E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 5 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 303.29 PRESS = 0.0 - Etot = -8229.4771 EKtot = 1918.0479 EPtot = -10147.5250 - BOND = 27.8635 ANGLE = 57.3314 DIHED = 76.4742 - 1-4 NB = 33.7232 1-4 EEL = 531.7330 VDWAALS = 1460.5572 - EELEC = -12335.2075 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1272E-03 - TEMP0 = 320.0000 REPNUM = 4 EXCHANGE# = 6 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.037 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 320.17 PRESS = 0.0 + Etot = -7987.2813 EKtot = 2024.8462 EPtot = -10012.1275 + BOND = 30.8420 ANGLE = 61.4213 DIHED = 85.7582 + 1-4 NB = 36.2938 1-4 EEL = 537.9794 VDWAALS = 1432.0555 + EELEC = -12196.4951 EHBOND = 0.0000 RESTRAINT = 0.0174 + EAMBER (non-restraint) = -10012.1449 + Ewald error estimate: 0.1312E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 6 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 300.34 PRESS = 0.0 - Etot = -8299.0101 EKtot = 1899.4251 EPtot = -10198.4352 - BOND = 21.8717 ANGLE = 61.2857 DIHED = 78.1464 - 1-4 NB = 32.0572 1-4 EEL = 539.2109 VDWAALS = 1448.9261 - EELEC = -12379.9333 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1042E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 7 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.017 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 314.71 PRESS = 0.0 + Etot = -7985.6224 EKtot = 1990.2847 EPtot = -9975.9071 + BOND = 31.0696 ANGLE = 66.2422 DIHED = 78.3173 + 1-4 NB = 36.6610 1-4 EEL = 540.0590 VDWAALS = 1424.3549 + EELEC = -12152.6381 EHBOND = 0.0000 RESTRAINT = 0.0269 + EAMBER (non-restraint) = -9975.9340 + Ewald error estimate: 0.1265E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 7 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 288.86 PRESS = 0.0 - Etot = -8367.8617 EKtot = 1826.8343 EPtot = -10194.6961 - BOND = 30.4191 ANGLE = 51.5597 DIHED = 78.4469 - 1-4 NB = 31.7471 1-4 EEL = 540.4483 VDWAALS = 1430.3360 - EELEC = -12357.6531 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1557E-03 - TEMP0 = 300.0000 REPNUM = 4 EXCHANGE# = 8 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.027 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 311.83 PRESS = 0.0 + Etot = -7988.9257 EKtot = 1972.0752 EPtot = -9961.0009 + BOND = 25.9141 ANGLE = 70.6956 DIHED = 80.0198 + 1-4 NB = 38.9425 1-4 EEL = 535.0756 VDWAALS = 1375.5478 + EELEC = -12087.2326 EHBOND = 0.0000 RESTRAINT = 0.0363 + EAMBER (non-restraint) = -9961.0372 + Ewald error estimate: 0.6147E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 8 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 293.36 PRESS = 0.0 - Etot = -8366.3734 EKtot = 1855.2967 EPtot = -10221.6701 - BOND = 29.7211 ANGLE = 56.2695 DIHED = 76.2061 - 1-4 NB = 33.0774 1-4 EEL = 540.8327 VDWAALS = 1431.2136 - EELEC = -12388.9905 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2232E-03 - TEMP0 = 300.0000 REPNUM = 4 EXCHANGE# = 9 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.036 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 314.72 PRESS = 0.0 + Etot = -7989.3334 EKtot = 1990.3716 EPtot = -9979.7050 + BOND = 26.3346 ANGLE = 77.2965 DIHED = 76.4488 + 1-4 NB = 38.0978 1-4 EEL = 537.1933 VDWAALS = 1329.8156 + EELEC = -12064.9378 EHBOND = 0.0000 RESTRAINT = 0.0461 + EAMBER (non-restraint) = -9979.7511 + Ewald error estimate: 0.5486E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 9 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 286.98 PRESS = 0.0 - Etot = -8362.7053 EKtot = 1814.9323 EPtot = -10177.6376 - BOND = 33.8029 ANGLE = 61.0108 DIHED = 76.5955 - 1-4 NB = 35.3699 1-4 EEL = 538.4760 VDWAALS = 1455.4109 - EELEC = -12378.3036 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1977E-03 - TEMP0 = 300.0000 REPNUM = 4 EXCHANGE# = 10 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.046 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 320.97 PRESS = 0.0 + Etot = -8001.7939 EKtot = 2029.8642 EPtot = -10031.6580 + BOND = 25.6569 ANGLE = 67.5005 DIHED = 72.4776 + 1-4 NB = 35.4194 1-4 EEL = 538.0291 VDWAALS = 1314.7280 + EELEC = -12085.5257 EHBOND = 0.0000 RESTRAINT = 0.0560 + EAMBER (non-restraint) = -10031.7141 + Ewald error estimate: 0.7120E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 10 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.056 + BBMD : 0.000 STSM : 0.000 +=============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.27% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.26% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.29 (90.83% of List ) -| Other 0.03 ( 9.17% of List ) -| List time 0.32 ( 9.53% of Nonbo) -| Short_ene time 2.28 (99.15% of Direc) -| Other 0.02 ( 0.85% of Direc) -| Direct Ewald time 2.29 (76.71% of Ewald) -| Adjust Ewald time 0.02 ( 0.61% of Ewald) +| Build the list 0.46 (95.47% of List ) +| Other 0.02 ( 4.53% of List ) +| List time 0.48 (23.11% of Nonbo) +| Short_ene time 1.12 (97.89% of Direc) +| Other 0.02 ( 2.11% of Direc) +| Direct Ewald time 1.14 (71.24% of Ewald) +| Adjust Ewald time 0.01 ( 0.52% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.03 ( 4.09% of Recip) -| Fill charge grid 0.05 ( 7.53% of Recip) -| Scalar sum 0.28 (40.87% of Recip) -| Grad sum 0.11 (16.17% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.21 (100.0% of FFT t) -| FFT time 0.21 (31.30% of Recip) -| Other 0.00 ( 0.04% of Recip) -| Recip Ewald time 0.67 (22.53% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.05% of Ewald) +| Fill Bspline coeffs 0.03 ( 6.62% of Recip) +| Fill charge grid 0.03 ( 7.53% of Recip) +| Scalar sum 0.12 (28.14% of Recip) +| Grad sum 0.07 (17.23% of Recip) +| FFT back comm time 0.01 ( 7.95% of FFT t) +| Other 0.16 (92.05% of FFT t) +| FFT time 0.17 (40.12% of Recip) +| Other 0.00 ( 0.37% of Recip) +| Recip Ewald time 0.43 (26.59% of Ewald) +| Force Adjust 0.02 ( 1.44% of Ewald) +| Virial junk 0.00 ( 0.14% of Ewald) | Other 0.00 ( 0.07% of Ewald) -| Ewald time 2.99 (90.46% of Nonbo) -| Nonbond force 3.31 (85.21% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.42% of Force) -| Other 0.56 (14.37% of Force) -| Force time 3.88 (97.01% of Runmd) -| Shake time 0.02 ( 0.42% of Runmd) -| Verlet update time 0.09 ( 2.22% of Runmd) -| Other 0.01 ( 0.35% of Runmd) -| Runmd Time 4.00 (98.48% of Total) -| Other 0.05 ( 1.24% of Total) -| Total time 4.06 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Ewald time 1.60 (76.89% of Nonbo) +| Nonbond force 2.08 (98.39% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.39% of Force) +| FRC Collect time 0.00 ( 0.14% of Force) +| Other 0.02 ( 1.08% of Force) +| Force time 2.11 (95.50% of Runmd) +| Shake time 0.01 ( 0.24% of Runmd) +| Verlet update time 0.07 ( 3.19% of Runmd) +| CRD distribute time 0.00 ( 0.03% of Runmd) +| Other 0.02 ( 1.05% of Runmd) +| Runmd Time 2.21 (97.18% of Total) +| Other 0.06 ( 2.55% of Total) +| Total time 2.28 (100.0% of ALL ) + +| Number of list builds : 18 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 4.00 Per Step(ms) = 80.01 -| ns/day = 2.16 seconds/ns = 40006.86 +| Elapsed(s) = 2.21 Per Step(ms) = 44.30 +| ns/day = 3.90 seconds/ns = 22147.77 | ----------------------------------------------------- -| Job began at 18:10:29.129 on 06/14/2016 -| Setup done at 18:10:29.192 on 06/14/2016 -| Run done at 18:10:33.192 on 06/14/2016 -| wallclock() was called 3211 times +| Job began at 19:19:01.412 on 09/21/2018 +| Setup done at 19:19:01.477 on 09/21/2018 +| Run done at 19:19:03.692 on 09/21/2018 +| wallclock() was called 3777 times diff --git test/nfe/abremd/save/rem.log test/nfe/abremd/save/rem.log index bd5b82e4d8..18a552b544 100644 --- test/nfe/abremd/save/rem.log +++ test/nfe/abremd/save/rem.log @@ -3,54 +3,54 @@ # REMD filenames: # remlog= rem.log # remtype= rem.type -# Rep#, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate (i,i+1), ResStruct# +# Rep#, Neibr#, Temp0, PotE(x_1), PotE(x_2), left_fe, right_fe, Success, Success rate (i,i+1) # exchange 1 - 1 0.98 0.00 -10152.55 320.00 310.00 0.00 -1 - 2 -1.00 0.00 -10313.68 300.00 300.00 0.00 -1 - 3 -1.00 0.00 -10131.41 330.00 330.00 0.00 -1 - 4 1.02 0.00 -10184.84 310.00 320.00 2.00 -1 + 1 4 300.00 -10152.55 -10184.84 0.00 0.00 T 0.00 + 2 3 310.00 -10313.68 -10131.41 0.00 0.00 F 0.00 + 3 2 320.00 -10131.41 -10313.68 0.00 0.00 F 0.00 + 4 1 330.00 -10184.84 -10152.55 0.00 0.00 T 2.00 # exchange 2 - 1 -1.00 302.81 -10151.37 310.00 310.00 1.00 -1 - 2 -1.00 295.85 -10314.14 300.00 300.00 0.00 -1 - 3 -1.00 310.03 -10095.05 330.00 330.00 0.00 -1 - 4 -1.00 309.86 -10209.95 320.00 320.00 0.00 -1 + 1 2 300.00 -10291.32 -10313.84 0.00 0.01 T 1.00 + 2 1 310.00 -10313.84 -10291.33 0.00 0.00 T 0.00 + 3 4 320.00 -10095.27 -10055.89 0.00 0.00 T 1.00 + 4 3 330.00 -10055.88 -10095.27 0.01 0.00 T 1.00 # exchange 3 - 1 1.02 303.93 -10187.24 310.00 320.00 1.33 -1 - 2 -1.00 289.48 -10273.64 300.00 300.00 0.00 -1 - 3 -1.00 304.61 -10071.59 330.00 330.00 0.00 -1 - 4 0.98 301.97 -10132.69 320.00 310.00 0.00 -1 + 1 4 300.00 -10289.45 -10051.82 0.01 0.01 F 0.67 + 2 3 310.00 -10225.31 -10094.44 0.00 0.00 F 0.00 + 3 2 320.00 -10094.44 -10225.31 0.00 0.00 F 0.67 + 4 1 330.00 -10051.81 -10289.46 0.01 0.00 F 0.67 # exchange 4 - 1 -1.00 315.20 -10174.73 320.00 320.00 0.00 -1 - 2 -1.00 284.89 -10238.21 300.00 300.00 0.00 -1 - 3 -1.00 311.68 -10078.78 330.00 330.00 0.00 -1 - 4 -1.00 291.69 -10150.19 310.00 310.00 1.00 -1 + 1 2 300.00 -10265.73 -10206.90 0.01 0.01 F 0.50 + 2 1 310.00 -10206.90 -10265.74 0.00 0.00 F 0.00 + 3 4 320.00 -10099.75 -10050.52 0.00 -0.00 F 0.50 + 4 3 330.00 -10050.51 -10099.74 0.01 0.00 F 0.50 # exchange 5 - 1 0.98 307.66 -10148.54 320.00 310.00 0.00 -1 - 2 -1.00 290.14 -10290.47 300.00 300.00 0.00 -1 - 3 -1.00 307.52 -10056.02 330.00 330.00 0.00 -1 - 4 1.02 294.60 -10149.65 310.00 320.00 1.20 -1 + 1 4 300.00 -10300.03 -10043.42 0.01 0.01 F 0.40 + 2 3 310.00 -10208.61 -10079.60 0.00 0.01 F 0.00 + 3 2 320.00 -10079.59 -10208.63 0.00 -0.00 F 0.40 + 4 1 330.00 -10043.40 -10300.06 0.01 0.01 F 0.40 # exchange 6 - 1 -1.00 298.35 -10163.88 310.00 310.00 1.00 -1 - 2 -1.00 288.76 -10262.02 300.00 300.00 0.00 -1 - 3 -1.00 315.05 -10089.80 330.00 330.00 0.00 -1 - 4 -1.00 305.84 -10148.06 320.00 320.00 0.00 -1 + 1 2 300.00 -10260.87 -10235.22 0.01 0.02 T 0.67 + 2 1 310.00 -10235.21 -10260.91 0.00 0.01 T 0.00 + 3 4 320.00 -10055.90 -10067.56 0.00 -0.00 T 0.67 + 4 3 330.00 -10067.53 -10055.90 0.02 0.01 T 0.33 # exchange 7 - 1 1.02 299.02 -10155.03 310.00 320.00 1.14 -1 - 2 -1.00 285.36 -10235.96 300.00 300.00 0.00 -1 - 3 -1.00 312.48 -10068.46 330.00 330.00 0.00 -1 - 4 0.98 303.29 -10158.02 320.00 310.00 0.00 -1 + 1 4 300.00 -10252.58 -10006.47 0.01 0.02 F 0.57 + 2 3 310.00 -10220.98 -10083.99 0.00 0.01 F 0.00 + 3 2 320.00 -10083.98 -10220.99 0.00 -0.00 F 0.57 + 4 1 330.00 -10006.45 -10252.59 0.02 0.01 F 0.29 # exchange 8 - 1 -1.00 299.20 -10087.87 320.00 320.00 0.00 -1 - 2 1.02 285.62 -10225.60 300.00 310.00 0.25 -1 - 3 -1.00 310.75 -10048.04 330.00 330.00 0.00 -1 - 4 0.98 300.34 -10198.88 310.00 300.00 1.00 -1 + 1 2 300.00 -10287.32 -10214.16 0.01 0.02 F 0.50 + 2 1 310.00 -10214.18 -10287.33 -0.00 0.01 F 0.00 + 3 4 320.00 -10080.96 -9981.16 0.00 -0.01 F 0.50 + 4 3 330.00 -9981.14 -10080.93 0.02 0.01 F 0.25 # exchange 9 - 1 -1.00 293.50 -10064.82 320.00 320.00 0.00 -1 - 2 -1.00 295.09 -10234.40 310.00 310.00 0.89 -1 - 3 -1.00 313.49 -10086.46 330.00 330.00 0.00 -1 - 4 -1.00 288.86 -10208.24 300.00 300.00 0.22 -1 + 1 4 300.00 -10235.26 -9966.66 0.02 0.02 F 0.44 + 2 3 310.00 -10239.90 -10078.44 -0.00 0.01 F 0.00 + 3 2 320.00 -10078.43 -10239.92 0.00 -0.01 F 0.44 + 4 1 330.00 -9966.62 -10235.30 0.02 0.02 F 0.22 # exchange 10 - 1 -1.00 296.71 -10076.82 320.00 320.00 0.00 -1 - 2 -1.00 287.97 -10194.77 310.00 310.00 0.80 -1 - 3 -1.00 313.18 -10063.12 330.00 330.00 0.00 -1 - 4 -1.00 293.36 -10222.47 300.00 300.00 0.20 -1 + 1 2 300.00 -10277.11 -10214.15 0.02 0.02 T 0.60 + 2 1 310.00 -10214.16 -10277.14 -0.00 0.01 T 0.00 + 3 4 320.00 -10067.13 -9991.05 0.00 -0.01 F 0.40 + 4 3 330.00 -9991.02 -10067.11 0.02 0.02 F 0.20 diff --git test/nfe/abremd/save/umbrella.1.ncdump test/nfe/abremd/save/umbrella.1.ncdump new file mode 100644 index 0000000000..37f6543aef --- /dev/null +++ test/nfe/abremd/save/umbrella.1.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0193969278, 0.0556426666, 0.0450832017, + 0.0048912701, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0085672554, 0.0465833051, 0.0526831603, + 0.0170234961, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/abremd/save/umbrella.2.ncdump test/nfe/abremd/save/umbrella.2.ncdump new file mode 100644 index 0000000000..b020b3c015 --- /dev/null +++ test/nfe/abremd/save/umbrella.2.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0080522420, 0.0270765434, 0.0238521115, + 0.0036018060, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0077385102, 0.0258582754, 0.0238881602, + 0.0049648566, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/abremd/save/umbrella.3.ncdump test/nfe/abremd/save/umbrella.3.ncdump new file mode 100644 index 0000000000..372ac6b390 --- /dev/null +++ test/nfe/abremd/save/umbrella.3.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0044904306, + 0.0113653507, 0.0085142959, 0.0006009205, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0015282668, + 0.0119615770, 0.0164802005, 0.0073936860, 0.0000101471, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/abremd/save/umbrella.4.ncdump test/nfe/abremd/save/umbrella.4.ncdump new file mode 100644 index 0000000000..12edc059b0 --- /dev/null +++ test/nfe/abremd/save/umbrella.4.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0125597366, + 0.0592567224, 0.0619041811, 0.0163401983, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0093433960, + 0.0407045784, 0.0407072434, 0.0093595452, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/bbmd/run-pmemd.sh test/nfe/bbmd/run-pmemd.sh index d0536704e0..c8bd686ecc 100755 --- test/nfe/bbmd/run-pmemd.sh +++ test/nfe/bbmd/run-pmemd.sh @@ -17,7 +17,7 @@ if test $? -ne 0; then fi set_SANDER pmemd.MPI -set_SANDER_CMD_FIX 8 +set_SANDER_CMD 4 JUNK="bbmd.log bbmd.?.txt umbrella.?.nc mdout.? inpcrd.? wt_umbrella.?.nc" JUNK="${JUNK} mt19937.nc restrt.? mdcrd.? groups prmtop sander.out logfile.*" @@ -40,22 +40,23 @@ cp -p ../prmtop ../inpcrd.? ../groups ../mt19937.nc . ${SANDER_CMD} -ng 4 -groupfile groups > sander.out 2>&1 -../../dacdif -t 1 save.pmemd/bbmd.log bbmd.log +# for mdout, use save.pmemd, others same with sander +../../dacdif -t 1 save.sander/bbmd.log bbmd.log -../../dacdif save.pmemd/mt19937.nc mt19937.nc +../../dacdif save.sander/mt19937.nc mt19937.nc for i in 1 2 3 4; do - ../../dacdif -t 2 save.pmemd/bbmd.$i.txt bbmd.$i.txt + ../../dacdif -t 2 save.sander/bbmd.$i.txt bbmd.$i.txt ../../dacdif -t 1 save.pmemd/mdout.$i mdout.$i done for i in 1 2 3; do - do_ncdump '%14.10f' save.pmemd/umbrella.$i.nc umbrella.$i.save.ncdump + do_ncdump '%14.10f' save.sander/umbrella.$i.nc umbrella.$i.save.ncdump do_ncdump '%14.10f' umbrella.$i.nc umbrella.$i.ncdump ../../dacdif umbrella.$i.save.ncdump umbrella.$i.ncdump done -do_ncdump '%14.10f ' save.pmemd/wt_umbrella.1.nc wt_umbrella.1.save.ncdump +do_ncdump '%14.10f ' save.sander/wt_umbrella.1.nc wt_umbrella.1.save.ncdump do_ncdump '%14.10f ' wt_umbrella.1.nc wt_umbrella.1.ncdump ../../dacdif -r 1.0e-4 wt_umbrella.1.save.ncdump wt_umbrella.1.ncdump diff --git test/nfe/bbmd/save.pmemd/mdout.1 test/nfe/bbmd/save.pmemd/mdout.1 index b1fed3dbea..b3efad9635 100644 --- test/nfe/bbmd/save.pmemd/mdout.1 +++ test/nfe/bbmd/save.pmemd/mdout.1 @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 03/04/2018 at 02:40:16 +| Run on 09/21/2018 at 15:19:59 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/bbmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/bbmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -249,116 +249,160 @@ NGLY NFE : BBMD : exchanged coordinates/velocities with 4 at t = 0.006 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 276.89 PRESS = 0.0 - Etot = -8491.2704 EKtot = 1751.1221 EPtot = -10242.3925 + Etot = -8491.2684 EKtot = 1751.1221 EPtot = -10242.3905 BOND = 18.6435 ANGLE = 62.5931 DIHED = 72.5964 1-4 NB = 31.9197 1-4 EEL = 541.0122 VDWAALS = 1296.4486 - EELEC = -12265.6060 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12265.6060 EHBOND = 0.0000 RESTRAINT = 0.0020 + EAMBER (non-restraint) = -10242.3925 Ewald error estimate: 0.5615E-03 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 287.96 PRESS = 0.0 - Etot = -8496.8594 EKtot = 1821.1252 EPtot = -10317.9846 - BOND = 24.2205 ANGLE = 66.3614 DIHED = 72.1252 - 1-4 NB = 33.9358 1-4 EEL = 541.6374 VDWAALS = 1314.7485 - EELEC = -12371.0134 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3109E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.002 STSM : 0.000 +=============================================================================== + NFE : BBMD : exchanged coordinates/velocities with 2 at t = 0.012 + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 297.05 PRESS = 0.0 + Etot = -8448.4741 EKtot = 1878.6022 EPtot = -10327.0763 + BOND = 22.1861 ANGLE = 76.4768 DIHED = 67.7863 + 1-4 NB = 30.4592 1-4 EEL = 521.1567 VDWAALS = 1370.6681 + EELEC = -12415.8152 EHBOND = 0.0000 RESTRAINT = 0.0059 + EAMBER (non-restraint) = -10327.0822 + Ewald error estimate: 0.1119E-03 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 282.76 PRESS = 0.0 - Etot = -8485.6092 EKtot = 1788.2700 EPtot = -10273.8791 - BOND = 24.4141 ANGLE = 65.6313 DIHED = 75.3836 - 1-4 NB = 31.4169 1-4 EEL = 535.3126 VDWAALS = 1335.9802 - EELEC = -12342.0178 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1162E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.006 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 294.72 PRESS = 0.0 + Etot = -8441.5858 EKtot = 1863.8779 EPtot = -10305.4636 + BOND = 27.9004 ANGLE = 70.6836 DIHED = 64.7798 + 1-4 NB = 30.4185 1-4 EEL = 520.4659 VDWAALS = 1362.0242 + EELEC = -12381.7516 EHBOND = 0.0000 RESTRAINT = 0.0156 + EAMBER (non-restraint) = -10305.4792 + Ewald error estimate: 0.2500E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 285.25 PRESS = 0.0 - Etot = -8475.9477 EKtot = 1803.9621 EPtot = -10279.9098 - BOND = 31.3991 ANGLE = 65.9274 DIHED = 72.0660 - 1-4 NB = 28.3690 1-4 EEL = 536.6874 VDWAALS = 1359.1876 - EELEC = -12373.5463 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4524E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.016 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 294.56 PRESS = 0.0 + Etot = -8439.7707 EKtot = 1862.8988 EPtot = -10302.6695 + BOND = 34.3968 ANGLE = 66.7156 DIHED = 72.2732 + 1-4 NB = 30.1853 1-4 EEL = 525.2221 VDWAALS = 1372.7267 + EELEC = -12404.2148 EHBOND = 0.0000 RESTRAINT = 0.0256 + EAMBER (non-restraint) = -10302.6951 + Ewald error estimate: 0.1765E-03 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 288.14 PRESS = 0.0 - Etot = -8475.7368 EKtot = 1822.2596 EPtot = -10297.9964 - BOND = 33.9948 ANGLE = 68.5312 DIHED = 72.7110 - 1-4 NB = 28.8050 1-4 EEL = 538.9621 VDWAALS = 1381.5447 - EELEC = -12422.5453 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8085E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.026 STSM : 0.000 +=============================================================================== + NFE : BBMD : exchanged coordinates/velocities with 2 at t = 0.048 + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 284.04 PRESS = 0.0 + Etot = -8473.9026 EKtot = 1796.3611 EPtot = -10270.2638 + BOND = 34.5054 ANGLE = 69.4641 DIHED = 73.0134 + 1-4 NB = 28.8336 1-4 EEL = 538.8999 VDWAALS = 1391.7689 + EELEC = -12406.7539 EHBOND = 0.0000 RESTRAINT = 0.0049 + EAMBER (non-restraint) = -10270.2686 + Ewald error estimate: 0.7482E-04 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 294.85 PRESS = 0.0 - Etot = -8468.8868 EKtot = 1864.6955 EPtot = -10333.5823 - BOND = 31.8837 ANGLE = 62.3381 DIHED = 73.4416 - 1-4 NB = 30.0994 1-4 EEL = 534.5969 VDWAALS = 1387.5823 - EELEC = -12453.5243 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1538E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.005 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 294.10 PRESS = 0.0 + Etot = -8467.0762 EKtot = 1859.9883 EPtot = -10327.0645 + BOND = 32.0118 ANGLE = 62.6637 DIHED = 73.4119 + 1-4 NB = 30.0883 1-4 EEL = 534.5478 VDWAALS = 1393.6709 + EELEC = -12453.4731 EHBOND = 0.0000 RESTRAINT = 0.0141 + EAMBER (non-restraint) = -10327.0786 + Ewald error estimate: 0.1285E-03 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 283.80 PRESS = 0.0 - Etot = -8471.4089 EKtot = 1794.8097 EPtot = -10266.2186 - BOND = 23.1318 ANGLE = 68.8595 DIHED = 72.7555 - 1-4 NB = 30.0002 1-4 EEL = 531.2118 VDWAALS = 1396.5285 - EELEC = -12388.7060 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1519E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.014 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 283.48 PRESS = 0.0 + Etot = -8469.6226 EKtot = 1792.7905 EPtot = -10262.4131 + BOND = 23.1249 ANGLE = 69.0577 DIHED = 72.8435 + 1-4 NB = 29.9632 1-4 EEL = 531.2127 VDWAALS = 1396.0513 + EELEC = -12384.6882 EHBOND = 0.0000 RESTRAINT = 0.0218 + EAMBER (non-restraint) = -10262.4349 + Ewald error estimate: 0.6819E-05 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 289.64 PRESS = 0.0 - Etot = -8474.3082 EKtot = 1831.7289 EPtot = -10306.0371 - BOND = 26.6518 ANGLE = 61.6608 DIHED = 73.9311 - 1-4 NB = 34.3165 1-4 EEL = 530.9909 VDWAALS = 1401.0300 - EELEC = -12434.6182 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2315E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.022 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 289.05 PRESS = 0.0 + Etot = -8472.2979 EKtot = 1827.9912 EPtot = -10300.2891 + BOND = 26.6570 ANGLE = 61.7091 DIHED = 74.0068 + 1-4 NB = 34.3318 1-4 EEL = 531.0221 VDWAALS = 1396.0191 + EELEC = -12424.0683 EHBOND = 0.0000 RESTRAINT = 0.0333 + EAMBER (non-restraint) = -10300.3224 + Ewald error estimate: 0.3187E-04 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 287.40 PRESS = 0.0 - Etot = -8477.0938 EKtot = 1817.5859 EPtot = -10294.6796 - BOND = 28.1846 ANGLE = 57.2104 DIHED = 73.5270 - 1-4 NB = 35.2470 1-4 EEL = 533.0285 VDWAALS = 1402.5424 - EELEC = -12424.4196 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2179E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.033 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 287.10 PRESS = 0.0 + Etot = -8475.0789 EKtot = 1815.6797 EPtot = -10290.7587 + BOND = 28.1859 ANGLE = 57.2634 DIHED = 73.6441 + 1-4 NB = 35.2456 1-4 EEL = 533.1050 VDWAALS = 1395.9776 + EELEC = -12414.2220 EHBOND = 0.0000 RESTRAINT = 0.0418 + EAMBER (non-restraint) = -10290.8005 + Ewald error estimate: 0.1738E-03 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 293.53 PRESS = 0.0 - Etot = -8477.7894 EKtot = 1856.3585 EPtot = -10334.1479 - BOND = 21.9363 ANGLE = 67.8844 DIHED = 70.7296 - 1-4 NB = 34.8187 1-4 EEL = 534.8662 VDWAALS = 1392.3618 - EELEC = -12456.7449 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1127E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.042 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 293.47 PRESS = 0.0 + Etot = -8475.8438 EKtot = 1855.9563 EPtot = -10331.8001 + BOND = 22.0162 ANGLE = 68.0704 DIHED = 70.8002 + 1-4 NB = 34.8321 1-4 EEL = 534.9337 VDWAALS = 1386.0635 + EELEC = -12448.5688 EHBOND = 0.0000 RESTRAINT = 0.0525 + EAMBER (non-restraint) = -10331.8527 + Ewald error estimate: 0.1188E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.053 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 287.02 PRESS = 0.0 - Etot = -8479.4911 EKtot = 1815.1917 EPtot = -10294.6828 - BOND = 26.4460 ANGLE = 64.6998 DIHED = 72.9267 - 1-4 NB = 31.8928 1-4 EEL = 535.8306 VDWAALS = 1366.7955 - EELEC = -12393.2742 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1638E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 288.19 PRESS = 0.0 + Etot = -8460.2291 EKtot = 1822.5612 EPtot = -10282.7903 + BOND = 26.6511 ANGLE = 65.2118 DIHED = 73.0812 + 1-4 NB = 31.9071 1-4 EEL = 535.8256 VDWAALS = 1368.2544 + EELEC = -12383.7408 EHBOND = 0.0000 RESTRAINT = 0.0194 + EAMBER (non-restraint) = -10282.8097 + Ewald error estimate: 0.1588E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 4.97 PRESS = 0.0 - Etot = 8.4721 EKtot = 31.4339 EPtot = 28.1941 - BOND = 4.6415 ANGLE = 3.5015 DIHED = 1.1860 - 1-4 NB = 2.4256 1-4 EEL = 3.5558 VDWAALS = 36.4722 - EELEC = 55.7017 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1583E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 5.38 PRESS = 0.0 + Etot = 23.9132 EKtot = 34.0178 EPtot = 31.2775 + BOND = 4.7484 ANGLE = 3.7545 DIHED = 1.2191 + 1-4 NB = 2.4311 1-4 EEL = 3.5398 VDWAALS = 35.2117 + EELEC = 55.8658 EHBOND = 0.0000 RESTRAINT = 0.0167 + EAMBER (non-restraint) = 31.2608 + Ewald error estimate: 0.1585E-03 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- @@ -369,47 +413,47 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.03 3.33 -| Nonbond 0.71 80.95 +| DataDistrib 0.01 1.21 +| Nonbond 0.84 84.98 | Bond 0.00 0.00 -| Angle 0.00 0.17 -| Dihedral 0.00 0.52 -| Shake 0.01 1.03 -| RunMD 0.12 13.77 -| Other 0.00 0.23 +| Angle 0.00 0.10 +| Dihedral 0.00 0.46 +| Shake 0.01 0.56 +| RunMD 0.12 12.29 +| Other 0.00 0.40 | ------------------------------ -| Total 0.87 +| Total 0.99 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.06 -| Build List 0.07 7.57 +| Set Up Cit 0.00 0.15 +| Build List 0.06 6.02 | --------------------------------- -| Total 0.07 7.63 +| Total 0.06 6.17 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.43 49.05 -| Exclude Masked 0.01 0.92 -| Other 0.00 0.57 +| NonBonded Calc 0.53 53.19 +| Exclude Masked 0.01 0.86 +| Other 0.01 0.86 | --------------------------------- -| Total 0.44 50.55 +| Total 0.54 54.90 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | 1D bspline 0.02 2.12 -| Grid Charges 0.02 2.18 -| Scalar Sum 0.03 3.04 -| Gradient Sum 0.02 2.18 -| FFT 0.12 13.25 +| Grid Charges 0.02 2.02 +| Scalar Sum 0.06 6.22 +| Gradient Sum 0.02 2.48 +| FFT 0.11 11.07 | --------------------------------- -| Total 0.20 22.78 +| Total 0.24 23.91 | PME Load Balancing CPU Time, Average for All Tasks: | @@ -424,17 +468,17 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.79 Per Step(ms) = 17.61 -| ns/day = 9.81 seconds/ns = 8804.55 +| Elapsed(s) = 0.89 Per Step(ms) = 19.69 +| ns/day = 8.77 seconds/ns = 9847.06 | | Average timings for all steps: -| Elapsed(s) = 0.89 Per Step(ms) = 17.81 -| ns/day = 9.70 seconds/ns = 8905.73 +| Elapsed(s) = 0.99 Per Step(ms) = 19.83 +| ns/day = 8.71 seconds/ns = 9916.83 | ----------------------------------------------------- -| Master Setup CPU time: 0.08 seconds -| Master NonSetup CPU time: 0.88 seconds -| Master Total CPU time: 0.97 seconds 0.00 hours +| Master Setup CPU time: 0.13 seconds +| Master NonSetup CPU time: 0.99 seconds +| Master Total CPU time: 1.12 seconds 0.00 hours | Master Setup wall time: 0 seconds | Master NonSetup wall time: 1 seconds diff --git test/nfe/bbmd/save.pmemd/mdout.2 test/nfe/bbmd/save.pmemd/mdout.2 index 6ef0f5c479..49e32999be 100644 --- test/nfe/bbmd/save.pmemd/mdout.2 +++ test/nfe/bbmd/save.pmemd/mdout.2 @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 01/18/2017 at 09:37:02 +| Run on 09/21/2018 at 15:19:59 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/bbmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/bbmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -170,7 +170,7 @@ NGLY | Dynamic Memory, Types Used: | Reals 245722 -| Integers 201281 +| Integers 210793 | Nonbonded Pairs Initial Allocation: 358302 @@ -256,116 +256,160 @@ NGLY NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 295.95 PRESS = 0.0 - Etot = -8385.6493 EKtot = 1871.6599 EPtot = -10257.3092 + Etot = -8385.6453 EKtot = 1871.6599 EPtot = -10257.3053 BOND = 21.9397 ANGLE = 68.0282 DIHED = 69.2900 1-4 NB = 32.7028 1-4 EEL = 521.1337 VDWAALS = 1390.4611 - EELEC = -12360.8648 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12360.8648 EHBOND = 0.0000 RESTRAINT = 0.0040 + EAMBER (non-restraint) = -10257.3092 Ewald error estimate: 0.2388E-03 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 304.83 PRESS = 0.0 - Etot = -8386.6115 EKtot = 1927.8105 EPtot = -10314.4220 - BOND = 22.6456 ANGLE = 77.7557 DIHED = 68.0261 - 1-4 NB = 30.4802 1-4 EEL = 521.1798 VDWAALS = 1371.8337 - EELEC = -12406.3432 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.9985E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.004 STSM : 0.000 +=============================================================================== + NFE : BBMD : exchanged coordinates/velocities with 1 at t = 0.012 + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 295.39 PRESS = 0.0 + Etot = -8437.2296 EKtot = 1868.1444 EPtot = -10305.3740 + BOND = 24.7287 ANGLE = 67.6278 DIHED = 72.4038 + 1-4 NB = 34.0088 1-4 EEL = 541.6417 VDWAALS = 1316.1134 + EELEC = -12361.9012 EHBOND = 0.0000 RESTRAINT = 0.0030 + EAMBER (non-restraint) = -10305.3770 + Ewald error estimate: 0.3189E-03 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 300.00 PRESS = 0.0 - Etot = -8379.0162 EKtot = 1897.2495 EPtot = -10276.2658 - BOND = 28.3361 ANGLE = 71.7148 DIHED = 64.9802 - 1-4 NB = 30.4650 1-4 EEL = 520.4301 VDWAALS = 1367.8604 - EELEC = -12360.0525 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2184E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.003 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 287.81 PRESS = 0.0 + Etot = -8425.2192 EKtot = 1820.1993 EPtot = -10245.4186 + BOND = 24.7555 ANGLE = 66.7336 DIHED = 75.7431 + 1-4 NB = 31.4573 1-4 EEL = 535.2650 VDWAALS = 1341.8806 + EELEC = -12321.2616 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10245.4265 + Ewald error estimate: 0.1311E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 300.13 PRESS = 0.0 - Etot = -8376.5983 EKtot = 1898.0840 EPtot = -10274.6823 - BOND = 35.0236 ANGLE = 67.4781 DIHED = 72.5306 - 1-4 NB = 30.2317 1-4 EEL = 525.2522 VDWAALS = 1382.3839 - EELEC = -12387.5824 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1880E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.008 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 290.53 PRESS = 0.0 + Etot = -8414.7515 EKtot = 1837.3792 EPtot = -10252.1307 + BOND = 31.8822 ANGLE = 66.9354 DIHED = 72.3486 + 1-4 NB = 28.3903 1-4 EEL = 536.6156 VDWAALS = 1368.5498 + EELEC = -12356.8653 EHBOND = 0.0000 RESTRAINT = 0.0127 + EAMBER (non-restraint) = -10252.1434 + Ewald error estimate: 0.4225E-04 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 298.92 PRESS = 0.0 - Etot = -8374.6955 EKtot = 1890.4669 EPtot = -10265.1624 - BOND = 25.5321 ANGLE = 70.9131 DIHED = 73.8081 - 1-4 NB = 29.7960 1-4 EEL = 526.8954 VDWAALS = 1415.2334 - EELEC = -12407.3406 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2003E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.013 STSM : 0.000 +=============================================================================== + NFE : BBMD : exchanged coordinates/velocities with 1 at t = 0.048 + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 303.27 PRESS = 0.0 + Etot = -8376.7226 EKtot = 1917.9797 EPtot = -10294.7023 + BOND = 25.1869 ANGLE = 70.1428 DIHED = 73.3947 + 1-4 NB = 29.7521 1-4 EEL = 526.8671 VDWAALS = 1404.3744 + EELEC = -12424.4262 EHBOND = 0.0000 RESTRAINT = 0.0058 + EAMBER (non-restraint) = -10294.7081 + Ewald error estimate: 0.1906E-03 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 299.92 PRESS = 0.0 - Etot = -8354.9732 EKtot = 1896.7645 EPtot = -10251.7377 - BOND = 38.6876 ANGLE = 77.1925 DIHED = 70.1409 - 1-4 NB = 28.7367 1-4 EEL = 523.6837 VDWAALS = 1444.3085 - EELEC = -12434.4876 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2765E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.006 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 300.76 PRESS = 0.0 + Etot = -8357.0365 EKtot = 1902.0540 EPtot = -10259.0904 + BOND = 38.6101 ANGLE = 77.0064 DIHED = 70.2016 + 1-4 NB = 28.7337 1-4 EEL = 523.5960 VDWAALS = 1438.3613 + EELEC = -12435.6103 EHBOND = 0.0000 RESTRAINT = 0.0108 + EAMBER (non-restraint) = -10259.1013 + Ewald error estimate: 0.2776E-03 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 283.81 PRESS = 0.0 - Etot = -8348.9691 EKtot = 1794.8783 EPtot = -10143.8474 - BOND = 35.6810 ANGLE = 79.3313 DIHED = 72.3605 - 1-4 NB = 28.4616 1-4 EEL = 525.6394 VDWAALS = 1456.5322 - EELEC = -12341.8533 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1786E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.011 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 283.94 PRESS = 0.0 + Etot = -8351.3158 EKtot = 1795.6965 EPtot = -10147.0123 + BOND = 35.5766 ANGLE = 79.2020 DIHED = 72.2858 + 1-4 NB = 28.4389 1-4 EEL = 525.6522 VDWAALS = 1458.1718 + EELEC = -12346.3554 EHBOND = 0.0000 RESTRAINT = 0.0158 + EAMBER (non-restraint) = -10147.0281 + Ewald error estimate: 0.1502E-03 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 295.21 PRESS = 0.0 - Etot = -8336.2921 EKtot = 1866.9886 EPtot = -10203.2807 - BOND = 38.9302 ANGLE = 74.6305 DIHED = 66.8105 - 1-4 NB = 29.2100 1-4 EEL = 519.8688 VDWAALS = 1441.3047 - EELEC = -12374.0354 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1913E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.016 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 295.65 PRESS = 0.0 + Etot = -8338.5813 EKtot = 1869.7395 EPtot = -10208.3208 + BOND = 38.9256 ANGLE = 74.6408 DIHED = 66.8360 + 1-4 NB = 29.2024 1-4 EEL = 519.8959 VDWAALS = 1447.5088 + EELEC = -12385.3511 EHBOND = 0.0000 RESTRAINT = 0.0208 + EAMBER (non-restraint) = -10208.3416 + Ewald error estimate: 0.2125E-03 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 296.29 PRESS = 0.0 - Etot = -8334.8695 EKtot = 1873.8336 EPtot = -10208.7031 - BOND = 30.0284 ANGLE = 78.0371 DIHED = 74.7571 - 1-4 NB = 28.1777 1-4 EEL = 515.9663 VDWAALS = 1417.7798 - EELEC = -12353.4495 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1903E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.021 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 296.94 PRESS = 0.0 + Etot = -8337.0843 EKtot = 1877.9218 EPtot = -10215.0061 + BOND = 30.0024 ANGLE = 78.2499 DIHED = 74.7666 + 1-4 NB = 28.1633 1-4 EEL = 516.0142 VDWAALS = 1425.5160 + EELEC = -12367.7441 EHBOND = 0.0000 RESTRAINT = 0.0257 + EAMBER (non-restraint) = -10215.0318 + Ewald error estimate: 0.1402E-03 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 300.67 PRESS = 0.0 - Etot = -8324.0327 EKtot = 1901.5060 EPtot = -10225.5387 - BOND = 31.7274 ANGLE = 62.3778 DIHED = 75.8193 - 1-4 NB = 29.9721 1-4 EEL = 515.7158 VDWAALS = 1393.4734 - EELEC = -12334.6245 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4141E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.026 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.35 PRESS = 0.0 + Etot = -8326.0828 EKtot = 1905.7867 EPtot = -10231.8695 + BOND = 31.7526 ANGLE = 62.2943 DIHED = 75.8211 + 1-4 NB = 29.9488 1-4 EEL = 515.8391 VDWAALS = 1400.7594 + EELEC = -12348.3156 EHBOND = 0.0000 RESTRAINT = 0.0308 + EAMBER (non-restraint) = -10231.9002 + Ewald error estimate: 0.5180E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.031 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 297.57 PRESS = 0.0 - Etot = -8360.1707 EKtot = 1881.9242 EPtot = -10242.0949 - BOND = 30.8532 ANGLE = 72.7459 DIHED = 70.8523 - 1-4 NB = 29.8234 1-4 EEL = 521.5765 VDWAALS = 1408.1171 - EELEC = -12376.0634 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1823E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 296.42 PRESS = 0.0 + Etot = -8380.2299 EKtot = 1874.6217 EPtot = -10254.8516 + BOND = 30.6477 ANGLE = 72.3440 DIHED = 70.7435 + 1-4 NB = 29.8005 1-4 EEL = 521.5843 VDWAALS = 1407.0572 + EELEC = -12387.0449 EHBOND = 0.0000 RESTRAINT = 0.0161 + EAMBER (non-restraint) = -10254.8677 + Ewald error estimate: 0.1800E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 5.30 PRESS = 0.0 - Etot = 22.0296 EKtot = 33.5397 EPtot = 45.6789 - BOND = 5.9180 ANGLE = 5.3076 DIHED = 3.3985 - 1-4 NB = 1.2427 1-4 EEL = 3.6491 VDWAALS = 30.0412 - EELEC = 30.5476 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.6366E-04 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 5.04 PRESS = 0.0 + Etot = 44.6213 EKtot = 31.8513 EPtot = 52.5232 + BOND = 5.9725 ANGLE = 5.3377 DIHED = 3.4015 + 1-4 NB = 1.2427 1-4 EEL = 3.6091 VDWAALS = 32.2842 + EELEC = 30.2041 EHBOND = 0.0000 RESTRAINT = 0.0090 + EAMBER (non-restraint) = 52.5142 + Ewald error estimate: 0.6527E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- @@ -376,47 +420,47 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.03 3.46 -| Nonbond 0.71 77.97 +| DataDistrib 0.01 1.42 +| Nonbond 0.82 83.35 | Bond 0.00 0.00 -| Angle 0.00 0.11 -| Dihedral 0.01 0.60 -| Shake 0.01 0.77 -| RunMD 0.14 15.71 -| Other 0.01 1.37 +| Angle 0.00 0.15 +| Dihedral 0.01 0.91 +| Shake 0.00 0.10 +| RunMD 0.14 13.71 +| Other 0.00 0.35 | ------------------------------ -| Total 0.91 +| Total 0.99 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.16 -| Build List 0.07 7.36 +| Set Up Cit 0.00 0.10 +| Build List 0.06 6.07 | --------------------------------- -| Total 0.07 7.53 +| Total 0.06 6.17 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.44 47.91 -| Exclude Masked 0.00 0.22 -| Other 0.01 0.93 +| NonBonded Calc 0.51 51.92 +| Exclude Masked 0.01 0.56 +| Other 0.01 0.76 | --------------------------------- -| Total 0.45 49.07 +| Total 0.53 53.24 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.02 2.42 -| Grid Charges 0.01 1.59 -| Scalar Sum 0.02 2.36 -| Gradient Sum 0.02 2.69 -| FFT 0.11 12.31 +| 1D bspline 0.03 2.88 +| Grid Charges 0.01 0.96 +| Scalar Sum 0.06 6.07 +| Gradient Sum 0.03 2.63 +| FFT 0.11 11.39 | --------------------------------- -| Total 0.19 21.37 +| Total 0.24 23.94 | PME Load Balancing CPU Time, Average for All Tasks: | @@ -431,18 +475,18 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.81 Per Step(ms) = 18.00 -| ns/day = 9.60 seconds/ns = 9001.98 +| Elapsed(s) = 0.88 Per Step(ms) = 19.64 +| ns/day = 8.80 seconds/ns = 9820.48 | | Average timings for all steps: -| Elapsed(s) = 0.91 Per Step(ms) = 18.27 -| ns/day = 9.46 seconds/ns = 9134.43 +| Elapsed(s) = 0.99 Per Step(ms) = 19.79 +| ns/day = 8.73 seconds/ns = 9896.43 | ----------------------------------------------------- -| Master Setup CPU time: 0.08 seconds -| Master NonSetup CPU time: 0.91 seconds -| Master Total CPU time: 0.99 seconds 0.00 hours +| Master Setup CPU time: 0.10 seconds +| Master NonSetup CPU time: 0.99 seconds +| Master Total CPU time: 1.09 seconds 0.00 hours -| Master Setup wall time: 1 seconds -| Master NonSetup wall time: 0 seconds +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds | Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/bbmd/save.pmemd/mdout.3 test/nfe/bbmd/save.pmemd/mdout.3 index 301b4a7ff4..f909466b11 100644 --- test/nfe/bbmd/save.pmemd/mdout.3 +++ test/nfe/bbmd/save.pmemd/mdout.3 @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 01/18/2017 at 09:37:02 +| Run on 09/21/2018 at 15:19:59 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/bbmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/bbmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -171,7 +171,7 @@ NGLY | Dynamic Memory, Types Used: | Reals 245730 -| Integers 202051 +| Integers 211563 | Nonbonded Pairs Initial Allocation: 358302 @@ -252,116 +252,160 @@ NGLY NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 298.88 PRESS = 0.0 - Etot = -8242.6824 EKtot = 1890.2031 EPtot = -10132.8855 + Etot = -8242.6798 EKtot = 1890.2031 EPtot = -10132.8829 BOND = 35.8714 ANGLE = 58.9761 DIHED = 71.9607 1-4 NB = 30.1761 1-4 EEL = 529.0867 VDWAALS = 1322.1277 - EELEC = -12181.0842 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12181.0842 EHBOND = 0.0000 RESTRAINT = 0.0026 + EAMBER (non-restraint) = -10132.8855 Ewald error estimate: 0.3336E-03 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.67 PRESS = 0.0 - Etot = -8230.3162 EKtot = 1920.4502 EPtot = -10150.7664 - BOND = 29.9122 ANGLE = 64.4342 DIHED = 72.3525 - 1-4 NB = 29.6110 1-4 EEL = 524.6633 VDWAALS = 1326.2167 - EELEC = -12197.9562 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4018E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.003 STSM : 0.000 +=============================================================================== + NFE : BBMD : exchanged coordinates/velocities with 4 at t = 0.012 + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 321.58 PRESS = 0.0 + Etot = -8063.9808 EKtot = 2033.7779 EPtot = -10097.7587 + BOND = 26.7320 ANGLE = 68.3762 DIHED = 76.8229 + 1-4 NB = 30.3875 1-4 EEL = 538.8947 VDWAALS = 1421.5697 + EELEC = -12260.5436 EHBOND = 0.0000 RESTRAINT = 0.0020 + EAMBER (non-restraint) = -10097.7606 + Ewald error estimate: 0.1519E-03 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 300.93 PRESS = 0.0 - Etot = -8226.2185 EKtot = 1903.1478 EPtot = -10129.3663 - BOND = 33.0576 ANGLE = 65.0494 DIHED = 71.0192 - 1-4 NB = 32.2831 1-4 EEL = 524.8455 VDWAALS = 1312.3354 - EELEC = -12167.9565 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2191E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.002 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 321.40 PRESS = 0.0 + Etot = -8072.1457 EKtot = 2032.5954 EPtot = -10104.7411 + BOND = 35.9385 ANGLE = 58.1162 DIHED = 81.0251 + 1-4 NB = 30.6838 1-4 EEL = 543.7134 VDWAALS = 1443.1021 + EELEC = -12297.3246 EHBOND = 0.0000 RESTRAINT = 0.0043 + EAMBER (non-restraint) = -10104.7454 + Ewald error estimate: 0.1799E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 300.82 PRESS = 0.0 - Etot = -8214.0622 EKtot = 1902.4586 EPtot = -10116.5208 - BOND = 36.3040 ANGLE = 47.8260 DIHED = 73.4749 - 1-4 NB = 32.7611 1-4 EEL = 527.0466 VDWAALS = 1304.2244 - EELEC = -12138.1578 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2083E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.004 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 315.45 PRESS = 0.0 + Etot = -8086.5961 EKtot = 1994.9816 EPtot = -10081.5777 + BOND = 28.8891 ANGLE = 57.5939 DIHED = 80.3435 + 1-4 NB = 34.8315 1-4 EEL = 539.7066 VDWAALS = 1449.0863 + EELEC = -12272.0353 EHBOND = 0.0000 RESTRAINT = 0.0067 + EAMBER (non-restraint) = -10081.5844 + Ewald error estimate: 0.1132E-03 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 304.73 PRESS = 0.0 - Etot = -8206.8582 EKtot = 1927.1927 EPtot = -10134.0508 - BOND = 31.3427 ANGLE = 62.0420 DIHED = 72.5182 - 1-4 NB = 33.9861 1-4 EEL = 528.8743 VDWAALS = 1306.1913 - EELEC = -12169.0055 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2677E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.007 STSM : 0.000 +=============================================================================== + NFE : BBMD : exchanged coordinates/velocities with 4 at t = 0.048 + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 300.61 PRESS = 0.0 + Etot = -8204.5870 EKtot = 1901.1429 EPtot = -10105.7299 + BOND = 31.7513 ANGLE = 62.7226 DIHED = 72.8048 + 1-4 NB = 34.0860 1-4 EEL = 528.8663 VDWAALS = 1316.1854 + EELEC = -12152.1483 EHBOND = 0.0000 RESTRAINT = 0.0021 + EAMBER (non-restraint) = -10105.7319 + Ewald error estimate: 0.2713E-03 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 298.22 PRESS = 0.0 - Etot = -8195.3792 EKtot = 1885.9947 EPtot = -10081.3739 - BOND = 36.1809 ANGLE = 62.6386 DIHED = 74.8690 - 1-4 NB = 34.4762 1-4 EEL = 530.9512 VDWAALS = 1315.0336 - EELEC = -12135.5235 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2534E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.002 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 297.47 PRESS = 0.0 + Etot = -8193.1320 EKtot = 1881.2533 EPtot = -10074.3853 + BOND = 36.2983 ANGLE = 62.7250 DIHED = 74.7227 + 1-4 NB = 34.5427 1-4 EEL = 530.9186 VDWAALS = 1320.2574 + EELEC = -12133.8565 EHBOND = 0.0000 RESTRAINT = 0.0065 + EAMBER (non-restraint) = -10074.3919 + Ewald error estimate: 0.2750E-03 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 299.90 PRESS = 0.0 - Etot = -8190.5587 EKtot = 1896.6539 EPtot = -10087.2126 - BOND = 33.2157 ANGLE = 61.1808 DIHED = 73.0610 - 1-4 NB = 33.7202 1-4 EEL = 528.2625 VDWAALS = 1318.7599 - EELEC = -12135.4127 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2148E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.007 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 299.71 PRESS = 0.0 + Etot = -8188.1042 EKtot = 1895.4631 EPtot = -10083.5672 + BOND = 33.2541 ANGLE = 61.1173 DIHED = 73.0462 + 1-4 NB = 33.7396 1-4 EEL = 528.2327 VDWAALS = 1317.2511 + EELEC = -12130.2170 EHBOND = 0.0000 RESTRAINT = 0.0088 + EAMBER (non-restraint) = -10083.5761 + Ewald error estimate: 0.2557E-03 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.36 PRESS = 0.0 - Etot = -8191.6004 EKtot = 1899.5201 EPtot = -10091.1205 - BOND = 25.1133 ANGLE = 57.3061 DIHED = 70.4452 - 1-4 NB = 32.8180 1-4 EEL = 537.6245 VDWAALS = 1324.4824 - EELEC = -12138.9100 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2084E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.009 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.18 PRESS = 0.0 + Etot = -8189.0498 EKtot = 1898.4208 EPtot = -10087.4707 + BOND = 25.0920 ANGLE = 57.1845 DIHED = 70.5873 + 1-4 NB = 32.8330 1-4 EEL = 537.5637 VDWAALS = 1318.6690 + EELEC = -12129.4132 EHBOND = 0.0000 RESTRAINT = 0.0129 + EAMBER (non-restraint) = -10087.4836 + Ewald error estimate: 0.4178E-04 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 304.35 PRESS = 0.0 - Etot = -8184.4834 EKtot = 1924.8070 EPtot = -10109.2905 - BOND = 35.0314 ANGLE = 64.2716 DIHED = 77.2769 - 1-4 NB = 31.6527 1-4 EEL = 539.1702 VDWAALS = 1322.4555 - EELEC = -12179.1488 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2059E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.013 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 304.07 PRESS = 0.0 + Etot = -8182.0304 EKtot = 1923.0347 EPtot = -10105.0651 + BOND = 35.0105 ANGLE = 64.0850 DIHED = 77.2842 + 1-4 NB = 31.6637 1-4 EEL = 539.1901 VDWAALS = 1315.4739 + EELEC = -12167.7879 EHBOND = 0.0000 RESTRAINT = 0.0154 + EAMBER (non-restraint) = -10105.0805 + Ewald error estimate: 0.3432E-04 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 307.95 PRESS = 0.0 - Etot = -8175.3727 EKtot = 1947.5452 EPtot = -10122.9179 - BOND = 24.4016 ANGLE = 71.2730 DIHED = 73.5781 - 1-4 NB = 36.4404 1-4 EEL = 529.0408 VDWAALS = 1311.8922 - EELEC = -12169.5439 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.7160E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.015 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 307.41 PRESS = 0.0 + Etot = -8172.9281 EKtot = 1944.1342 EPtot = -10117.0623 + BOND = 24.3915 ANGLE = 71.1044 DIHED = 73.6601 + 1-4 NB = 36.4353 1-4 EEL = 529.0825 VDWAALS = 1305.5854 + EELEC = -12157.3403 EHBOND = 0.0000 RESTRAINT = 0.0188 + EAMBER (non-restraint) = -10117.0810 + Ewald error estimate: 0.7498E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.019 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.98 PRESS = 0.0 - Etot = -8205.7532 EKtot = 1909.7973 EPtot = -10115.5505 - BOND = 32.0431 ANGLE = 61.4998 DIHED = 73.0556 - 1-4 NB = 32.7925 1-4 EEL = 529.9566 VDWAALS = 1316.3719 - EELEC = -12161.2699 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2012E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 303.14 PRESS = 0.0 + Etot = -8186.2647 EKtot = 1917.1481 EPtot = -10103.4128 + BOND = 32.2538 ANGLE = 61.7895 DIHED = 73.1561 + 1-4 NB = 32.8355 1-4 EEL = 529.9371 VDWAALS = 1317.4420 + EELEC = -12150.8334 EHBOND = 0.0000 RESTRAINT = 0.0067 + EAMBER (non-restraint) = -10103.4195 + Ewald error estimate: 0.2101E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 2.91 PRESS = 0.0 - Etot = 20.9054 EKtot = 18.4207 EPtot = 21.7626 - BOND = 4.1559 ANGLE = 5.8054 DIHED = 1.8574 - 1-4 NB = 1.9224 1-4 EEL = 4.6144 VDWAALS = 7.2657 - EELEC = 21.4401 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1214E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 4.19 PRESS = 0.0 + Etot = 23.4763 EKtot = 26.5188 EPtot = 19.9609 + BOND = 4.2041 ANGLE = 5.7902 DIHED = 1.7963 + 1-4 NB = 1.9257 1-4 EEL = 4.6212 VDWAALS = 5.4268 + EELEC = 21.7942 EHBOND = 0.0000 RESTRAINT = 0.0066 + EAMBER (non-restraint) = 19.9543 + Ewald error estimate: 0.1193E-03 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- @@ -372,73 +416,73 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.03 2.86 -| Nonbond 0.74 80.93 -| Bond 0.00 0.05 -| Angle 0.00 0.11 -| Dihedral 0.00 0.44 -| Shake 0.01 0.82 -| RunMD 0.12 13.35 -| Other 0.01 1.43 +| DataDistrib 0.02 2.12 +| Nonbond 0.87 88.02 +| Bond 0.00 0.00 +| Angle 0.00 0.05 +| Dihedral 0.00 0.25 +| Shake 0.01 0.66 +| RunMD 0.08 8.54 +| Other 0.00 0.35 | ------------------------------ -| Total 0.91 +| Total 0.99 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.00 -| Build List 0.07 7.75 +| Set Up Cit 0.00 0.10 +| Build List 0.06 6.01 | --------------------------------- -| Total 0.07 7.75 +| Total 0.06 6.11 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.43 47.14 -| Exclude Masked 0.01 1.15 -| Other 0.01 0.82 +| NonBonded Calc 0.53 53.41 +| Exclude Masked 0.01 0.91 +| Other 0.02 1.87 | --------------------------------- -| Total 0.45 49.12 +| Total 0.56 56.19 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.02 1.87 -| Grid Charges 0.02 1.98 -| Scalar Sum 0.03 3.13 -| Gradient Sum 0.02 2.31 -| FFT 0.13 14.72 +| 1D bspline 0.02 1.67 +| Grid Charges 0.02 2.22 +| Scalar Sum 0.06 5.61 +| Gradient Sum 0.02 2.32 +| FFT 0.14 13.90 | --------------------------------- -| Total 0.22 24.01 +| Total 0.25 25.72 | PME Load Balancing CPU Time, Average for All Tasks: | | Routine Sec % | ------------------------------------ | Atom Reassign 0.00 0.00 -| Image Reassign 0.00 0.05 +| Image Reassign 0.00 0.00 | FFT Reassign 0.00 0.00 | ------------------------------------ -| Total 0.00 0.05 +| Total 0.00 0.00 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.81 Per Step(ms) = 18.00 -| ns/day = 9.60 seconds/ns = 9002.47 +| Elapsed(s) = 0.88 Per Step(ms) = 19.64 +| ns/day = 8.80 seconds/ns = 9819.49 | | Average timings for all steps: -| Elapsed(s) = 0.92 Per Step(ms) = 18.31 -| ns/day = 9.44 seconds/ns = 9155.85 +| Elapsed(s) = 0.99 Per Step(ms) = 19.83 +| ns/day = 8.71 seconds/ns = 9916.69 | ----------------------------------------------------- -| Master Setup CPU time: 0.08 seconds -| Master NonSetup CPU time: 0.91 seconds -| Master Total CPU time: 1.00 seconds 0.00 hours +| Master Setup CPU time: 0.13 seconds +| Master NonSetup CPU time: 0.99 seconds +| Master Total CPU time: 1.12 seconds 0.00 hours -| Master Setup wall time: 1 seconds -| Master NonSetup wall time: 0 seconds +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds | Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/bbmd/save.pmemd/mdout.4 test/nfe/bbmd/save.pmemd/mdout.4 index 0181b85ffd..0be84d28cd 100644 --- test/nfe/bbmd/save.pmemd/mdout.4 +++ test/nfe/bbmd/save.pmemd/mdout.4 @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 01/18/2017 at 09:37:02 +| Run on 09/21/2018 at 15:19:59 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/bbmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/bbmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -167,7 +167,7 @@ NGLY | Dynamic Memory, Types Used: | Reals 245734 -| Integers 202929 +| Integers 212441 | Nonbonded Pairs Initial Allocation: 358302 @@ -261,108 +261,142 @@ NGLY Ewald error estimate: 0.2510E-03 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 329.68 PRESS = 0.0 - Etot = -7999.7042 EKtot = 2084.9632 EPtot = -10084.6674 - BOND = 27.2275 ANGLE = 69.4573 DIHED = 76.9850 - 1-4 NB = 30.4217 1-4 EEL = 538.8774 VDWAALS = 1423.2333 - EELEC = -12250.8696 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1474E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : BBMD : exchanged coordinates/velocities with 3 at t = 0.012 + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 311.09 PRESS = 0.0 + Etot = -8170.8095 EKtot = 1967.3943 EPtot = -10138.2037 + BOND = 30.5434 ANGLE = 65.5379 DIHED = 72.5651 + 1-4 NB = 29.6461 1-4 EEL = 524.6076 VDWAALS = 1327.4856 + EELEC = -12188.5894 EHBOND = 0.0000 RESTRAINT = 0.0000 + Ewald error estimate: 0.4085E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 326.98 PRESS = 0.0 - Etot = -8007.6047 EKtot = 2067.9145 EPtot = -10075.5193 - BOND = 36.3682 ANGLE = 58.8364 DIHED = 81.2109 - 1-4 NB = 30.7063 1-4 EEL = 543.7278 VDWAALS = 1450.2028 - EELEC = -12276.5717 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1510E-03 + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 305.94 PRESS = 0.0 + Etot = -8166.1719 EKtot = 1934.8274 EPtot = -10100.9993 + BOND = 33.5059 ANGLE = 66.0562 DIHED = 71.2302 + 1-4 NB = 32.3779 1-4 EEL = 524.7959 VDWAALS = 1317.9341 + EELEC = -12146.8994 EHBOND = 0.0000 RESTRAINT = 0.0000 + Ewald error estimate: 0.1985E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 321.08 PRESS = 0.0 - Etot = -8021.9247 EKtot = 2030.5729 EPtot = -10052.4976 - BOND = 29.2631 ANGLE = 58.2869 DIHED = 80.6033 - 1-4 NB = 34.9179 1-4 EEL = 539.7281 VDWAALS = 1459.9850 - EELEC = -12255.2818 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1245E-03 + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 306.06 PRESS = 0.0 + Etot = -8153.1540 EKtot = 1935.6074 EPtot = -10088.7613 + BOND = 36.8194 ANGLE = 48.3858 DIHED = 73.7001 + 1-4 NB = 32.8541 1-4 EEL = 527.0266 VDWAALS = 1313.4508 + EELEC = -12120.9981 EHBOND = 0.0000 RESTRAINT = 0.0000 + Ewald error estimate: 0.2068E-03 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 321.27 PRESS = 0.0 - Etot = -8014.9058 EKtot = 2031.7911 EPtot = -10046.6969 - BOND = 34.7877 ANGLE = 62.2897 DIHED = 82.9428 - 1-4 NB = 34.5576 1-4 EEL = 540.4726 VDWAALS = 1458.3627 - EELEC = -12260.1100 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8007E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : BBMD : exchanged coordinates/velocities with 3 at t = 0.048 + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 325.50 PRESS = 0.0 + Etot = -8017.9689 EKtot = 2058.5570 EPtot = -10076.5259 + BOND = 34.3682 ANGLE = 61.6542 DIHED = 82.6050 + 1-4 NB = 34.4701 1-4 EEL = 540.5039 VDWAALS = 1446.9701 + EELEC = -12277.0974 EHBOND = 0.0000 RESTRAINT = 0.0000 + Ewald error estimate: 0.5853E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 322.40 PRESS = 0.0 - Etot = -8015.9284 EKtot = 2038.9287 EPtot = -10054.8570 - BOND = 29.5668 ANGLE = 70.6741 DIHED = 81.3433 - 1-4 NB = 34.2873 1-4 EEL = 542.4777 VDWAALS = 1469.1213 - EELEC = -12282.3277 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1348E-03 + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 323.37 PRESS = 0.0 + Etot = -8019.2389 EKtot = 2045.0595 EPtot = -10064.2984 + BOND = 29.5388 ANGLE = 70.3839 DIHED = 81.3562 + 1-4 NB = 34.2449 1-4 EEL = 542.5258 VDWAALS = 1462.8336 + EELEC = -12285.1816 EHBOND = 0.0000 RESTRAINT = 0.0000 + Ewald error estimate: 0.1821E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 315.10 PRESS = 0.0 - Etot = -8012.6363 EKtot = 1992.7391 EPtot = -10005.3753 - BOND = 30.8147 ANGLE = 71.7439 DIHED = 80.2585 - 1-4 NB = 33.2160 1-4 EEL = 548.0500 VDWAALS = 1476.8746 - EELEC = -12246.3330 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4477E-03 + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 315.08 PRESS = 0.0 + Etot = -8015.9971 EKtot = 1992.6155 EPtot = -10008.6126 + BOND = 30.7758 ANGLE = 71.6675 DIHED = 80.1529 + 1-4 NB = 33.2178 1-4 EEL = 547.9964 VDWAALS = 1478.4399 + EELEC = -12250.8629 EHBOND = 0.0000 RESTRAINT = 0.0000 + Ewald error estimate: 0.4192E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 318.74 PRESS = 0.0 - Etot = -8004.7176 EKtot = 2015.7930 EPtot = -10020.5106 - BOND = 35.1029 ANGLE = 65.2070 DIHED = 77.3271 - 1-4 NB = 34.9870 1-4 EEL = 544.9059 VDWAALS = 1460.6786 - EELEC = -12238.7190 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2243E-03 + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 318.98 PRESS = 0.0 + Etot = -8008.2151 EKtot = 2017.2765 EPtot = -10025.4916 + BOND = 35.0349 ANGLE = 65.1058 DIHED = 77.2345 + 1-4 NB = 34.9578 1-4 EEL = 544.9452 VDWAALS = 1466.6778 + EELEC = -12249.4476 EHBOND = 0.0000 RESTRAINT = 0.0000 + Ewald error estimate: 0.2589E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 322.81 PRESS = 0.0 - Etot = -8000.2196 EKtot = 2041.5050 EPtot = -10041.7246 - BOND = 35.7169 ANGLE = 62.2294 DIHED = 71.8140 - 1-4 NB = 35.9199 1-4 EEL = 545.9610 VDWAALS = 1446.6623 - EELEC = -12240.0280 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4783E-04 + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 323.44 PRESS = 0.0 + Etot = -8003.8742 EKtot = 2045.5263 EPtot = -10049.4006 + BOND = 35.7349 ANGLE = 62.2572 DIHED = 71.7888 + 1-4 NB = 35.8927 1-4 EEL = 545.9371 VDWAALS = 1452.8739 + EELEC = -12253.8850 EHBOND = 0.0000 RESTRAINT = 0.0000 + Ewald error estimate: 0.2399E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 312.72 PRESS = 0.0 - Etot = -7999.8135 EKtot = 1977.7451 EPtot = -9977.5586 - BOND = 32.8641 ANGLE = 68.2270 DIHED = 74.7237 - 1-4 NB = 31.6469 1-4 EEL = 541.2326 VDWAALS = 1455.9853 - EELEC = -12182.2381 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2095E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 312.82 PRESS = 0.0 + Etot = -8003.8014 EKtot = 1978.3197 EPtot = -9982.1212 + BOND = 32.8596 ANGLE = 68.3026 DIHED = 74.7241 + 1-4 NB = 31.6094 1-4 EEL = 541.1627 VDWAALS = 1461.6834 + EELEC = -12192.4631 EHBOND = 0.0000 RESTRAINT = 0.0000 + Ewald error estimate: 0.2201E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 323.06 PRESS = 0.0 - Etot = -8007.0482 EKtot = 2043.1257 EPtot = -10050.1739 - BOND = 31.8020 ANGLE = 64.7040 DIHED = 78.8134 - 1-4 NB = 33.1517 1-4 EEL = 542.4825 VDWAALS = 1450.5021 - EELEC = -12251.6295 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1818E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 321.75 PRESS = 0.0 + Etot = -8028.4845 EKtot = 2034.8014 EPtot = -10063.2859 + BOND = 31.6181 ANGLE = 64.3546 DIHED = 78.6978 + 1-4 NB = 33.1152 1-4 EEL = 542.4777 VDWAALS = 1448.7152 + EELEC = -12262.2658 EHBOND = 0.0000 RESTRAINT = 0.0013 + EAMBER (non-restraint) = -10063.2872 + Ewald error estimate: 0.1859E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 7.33 PRESS = 0.0 - Etot = 8.6509 EKtot = 46.3741 EPtot = 43.1229 - BOND = 3.4733 ANGLE = 4.7888 DIHED = 3.3200 - 1-4 NB = 1.9593 1-4 EEL = 2.9370 VDWAALS = 20.6307 - EELEC = 27.9836 EHBOND = 0.0000 RESTRAINT = 0.0000 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 7.21 PRESS = 0.0 + Etot = 31.2702 EKtot = 45.5675 EPtot = 45.6772 + BOND = 3.4776 ANGLE = 4.8649 DIHED = 3.2667 + 1-4 NB = 1.9468 1-4 EEL = 2.9276 VDWAALS = 20.9036 + EELEC = 27.8820 EHBOND = 0.0000 RESTRAINT = 0.0023 + EAMBER (non-restraint) = 45.6750 Ewald error estimate: 0.1068E-03 ------------------------------------------------------------------------------ @@ -374,73 +408,73 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.05 5.47 -| Nonbond 0.74 81.38 -| Bond 0.00 0.00 -| Angle 0.00 0.06 -| Dihedral 0.01 0.66 -| Shake 0.01 0.88 -| RunMD 0.09 10.11 -| Other 0.01 1.44 +| DataDistrib 0.02 1.87 +| Nonbond 0.85 86.41 +| Bond 0.00 0.05 +| Angle 0.00 0.10 +| Dihedral 0.00 0.30 +| Shake 0.01 0.66 +| RunMD 0.10 10.26 +| Other 0.00 0.35 | ------------------------------ -| Total 0.90 +| Total 0.99 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 -| Build List 0.07 7.68 +| Build List 0.06 6.16 | --------------------------------- -| Total 0.07 7.68 +| Total 0.06 6.16 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.44 48.12 -| Exclude Masked 0.01 0.88 -| Other 0.00 0.50 +| NonBonded Calc 0.53 53.16 +| Exclude Masked 0.01 0.76 +| Other 0.01 0.61 | --------------------------------- -| Total 0.45 49.50 +| Total 0.54 54.52 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.01 1.16 -| Grid Charges 0.02 2.04 -| Scalar Sum 0.01 1.66 -| Gradient Sum 0.02 2.60 -| FFT 0.15 16.69 +| 1D bspline 0.01 1.31 +| Grid Charges 0.02 1.57 +| Scalar Sum 0.06 6.42 +| Gradient Sum 0.02 1.92 +| FFT 0.14 14.30 | --------------------------------- -| Total 0.22 24.14 +| Total 0.25 25.52 | PME Load Balancing CPU Time, Average for All Tasks: | | Routine Sec % | ------------------------------------ | Atom Reassign 0.00 0.00 -| Image Reassign 0.00 0.06 +| Image Reassign 0.00 0.20 | FFT Reassign 0.00 0.00 | ------------------------------------ -| Total 0.00 0.06 +| Total 0.00 0.20 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.81 Per Step(ms) = 18.02 -| ns/day = 9.59 seconds/ns = 9011.09 +| Elapsed(s) = 0.89 Per Step(ms) = 19.68 +| ns/day = 8.78 seconds/ns = 9839.09 | | Average timings for all steps: -| Elapsed(s) = 0.92 Per Step(ms) = 18.31 -| ns/day = 9.44 seconds/ns = 9156.40 +| Elapsed(s) = 0.99 Per Step(ms) = 19.84 +| ns/day = 8.71 seconds/ns = 9918.18 | ----------------------------------------------------- -| Master Setup CPU time: 0.08 seconds -| Master NonSetup CPU time: 0.91 seconds -| Master Total CPU time: 0.99 seconds 0.00 hours +| Master Setup CPU time: 0.13 seconds +| Master NonSetup CPU time: 0.99 seconds +| Master Total CPU time: 1.12 seconds 0.00 hours -| Master Setup wall time: 1 seconds -| Master NonSetup wall time: 0 seconds +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds | Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/bbmd/save.sander/mdout.1 test/nfe/bbmd/save.sander/mdout.1 index 32925e096f..f06a9aae4a 100644 --- test/nfe/bbmd/save.sander/mdout.1 +++ test/nfe/bbmd/save.sander/mdout.1 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 03/04/2018 at 02:46:02 +| Run on 09/21/2018 at 15:00:14 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/bbmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/bbmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -239,105 +239,146 @@ NGLY NFE : BBMD : exchanged coordinates/velocities with 4 at t = 0.006 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 276.89 PRESS = 0.0 - Etot = -8491.2704 EKtot = 1751.1221 EPtot = -10242.3925 + Etot = -8491.2684 EKtot = 1751.1221 EPtot = -10242.3905 BOND = 18.6435 ANGLE = 62.5931 DIHED = 72.5964 1-4 NB = 31.9197 1-4 EEL = 541.0122 VDWAALS = 1296.4486 - EELEC = -12265.6060 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12265.6060 EHBOND = 0.0000 RESTRAINT = 0.0020 + EAMBER (non-restraint) = -10242.3925 Ewald error estimate: 0.5615E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.002 STSM : 0.000 +=============================================================================== NFE : BBMD : exchanged coordinates/velocities with 2 at t = 0.012 NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 297.05 PRESS = 0.0 - Etot = -8448.4800 EKtot = 1878.6022 EPtot = -10327.0822 + Etot = -8448.4741 EKtot = 1878.6022 EPtot = -10327.0763 BOND = 22.1861 ANGLE = 76.4768 DIHED = 67.7863 1-4 NB = 30.4592 1-4 EEL = 521.1567 VDWAALS = 1370.6681 - EELEC = -12415.8152 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12415.8152 EHBOND = 0.0000 RESTRAINT = 0.0059 + EAMBER (non-restraint) = -10327.0822 Ewald error estimate: 0.1119E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.006 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 294.72 PRESS = 0.0 - Etot = -8441.6014 EKtot = 1863.8779 EPtot = -10305.4792 + Etot = -8441.5858 EKtot = 1863.8779 EPtot = -10305.4636 BOND = 27.9004 ANGLE = 70.6836 DIHED = 64.7798 1-4 NB = 30.4185 1-4 EEL = 520.4659 VDWAALS = 1362.0242 - EELEC = -12381.7516 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12381.7516 EHBOND = 0.0000 RESTRAINT = 0.0156 + EAMBER (non-restraint) = -10305.4792 Ewald error estimate: 0.2500E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.016 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 294.56 PRESS = 0.0 - Etot = -8439.7963 EKtot = 1862.8988 EPtot = -10302.6951 + Etot = -8439.7707 EKtot = 1862.8988 EPtot = -10302.6695 BOND = 34.3968 ANGLE = 66.7156 DIHED = 72.2732 1-4 NB = 30.1853 1-4 EEL = 525.2221 VDWAALS = 1372.7267 - EELEC = -12404.2148 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12404.2148 EHBOND = 0.0000 RESTRAINT = 0.0256 + EAMBER (non-restraint) = -10302.6951 Ewald error estimate: 0.1765E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.026 STSM : 0.000 +=============================================================================== NFE : BBMD : exchanged coordinates/velocities with 2 at t = 0.048 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 288.76 PRESS = 0.0 - Etot = -8444.1021 EKtot = 1826.1665 EPtot = -10270.2686 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 284.04 PRESS = 0.0 + Etot = -8473.9026 EKtot = 1796.3611 EPtot = -10270.2638 BOND = 34.5054 ANGLE = 69.4641 DIHED = 73.0134 1-4 NB = 28.8336 1-4 EEL = 538.8999 VDWAALS = 1391.7689 - EELEC = -12406.7539 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12406.7539 EHBOND = 0.0000 RESTRAINT = 0.0049 + EAMBER (non-restraint) = -10270.2686 Ewald error estimate: 0.7482E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.005 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 294.10 PRESS = 0.0 - Etot = -8467.0903 EKtot = 1859.9883 EPtot = -10327.0786 + Etot = -8467.0762 EKtot = 1859.9883 EPtot = -10327.0645 BOND = 32.0118 ANGLE = 62.6637 DIHED = 73.4119 1-4 NB = 30.0883 1-4 EEL = 534.5478 VDWAALS = 1393.6709 - EELEC = -12453.4731 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12453.4731 EHBOND = 0.0000 RESTRAINT = 0.0141 + EAMBER (non-restraint) = -10327.0786 Ewald error estimate: 0.1285E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.014 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 283.48 PRESS = 0.0 - Etot = -8469.6444 EKtot = 1792.7905 EPtot = -10262.4349 + Etot = -8469.6226 EKtot = 1792.7905 EPtot = -10262.4131 BOND = 23.1249 ANGLE = 69.0577 DIHED = 72.8435 1-4 NB = 29.9632 1-4 EEL = 531.2127 VDWAALS = 1396.0513 - EELEC = -12384.6882 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12384.6882 EHBOND = 0.0000 RESTRAINT = 0.0218 + EAMBER (non-restraint) = -10262.4349 Ewald error estimate: 0.6819E-05 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.022 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 289.05 PRESS = 0.0 - Etot = -8472.3312 EKtot = 1827.9912 EPtot = -10300.3224 + Etot = -8472.2979 EKtot = 1827.9912 EPtot = -10300.2891 BOND = 26.6570 ANGLE = 61.7091 DIHED = 74.0068 1-4 NB = 34.3318 1-4 EEL = 531.0221 VDWAALS = 1396.0191 - EELEC = -12424.0683 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12424.0683 EHBOND = 0.0000 RESTRAINT = 0.0333 + EAMBER (non-restraint) = -10300.3224 Ewald error estimate: 0.3187E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.033 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 287.10 PRESS = 0.0 - Etot = -8475.1208 EKtot = 1815.6797 EPtot = -10290.8005 + Etot = -8475.0789 EKtot = 1815.6797 EPtot = -10290.7587 BOND = 28.1859 ANGLE = 57.2634 DIHED = 73.6441 1-4 NB = 35.2456 1-4 EEL = 533.1050 VDWAALS = 1395.9776 - EELEC = -12414.2220 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12414.2220 EHBOND = 0.0000 RESTRAINT = 0.0418 + EAMBER (non-restraint) = -10290.8005 Ewald error estimate: 0.1738E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.042 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 293.47 PRESS = 0.0 - Etot = -8475.8963 EKtot = 1855.9563 EPtot = -10331.8527 + Etot = -8475.8438 EKtot = 1855.9563 EPtot = -10331.8001 BOND = 22.0162 ANGLE = 68.0704 DIHED = 70.8002 1-4 NB = 34.8321 1-4 EEL = 534.9337 VDWAALS = 1386.0635 - EELEC = -12448.5688 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12448.5688 EHBOND = 0.0000 RESTRAINT = 0.0525 + EAMBER (non-restraint) = -10331.8527 Ewald error estimate: 0.1188E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.053 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 50 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 289.55 PRESS = 0.0 - Etot = -8445.0374 EKtot = 1831.1899 EPtot = -10276.2274 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 289.28 PRESS = 0.0 + Etot = -8446.7283 EKtot = 1829.4815 EPtot = -10276.2098 BOND = 28.1241 ANGLE = 66.0009 DIHED = 73.1940 1-4 NB = 31.8542 1-4 EEL = 536.0749 VDWAALS = 1363.7516 - EELEC = -12375.2270 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12375.2270 EHBOND = 0.0000 RESTRAINT = 0.0176 + EAMBER (non-restraint) = -10276.2274 Ewald error estimate: 0.1731E-03 ------------------------------------------------------------------------------ @@ -345,11 +386,12 @@ NGLY R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 4.52 PRESS = 0.0 - Etot = 37.9393 EKtot = 28.5969 EPtot = 29.5000 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 5.07 PRESS = 0.0 + Etot = 38.3826 EKtot = 32.0556 EPtot = 29.4922 BOND = 4.4886 ANGLE = 4.3076 DIHED = 1.9364 1-4 NB = 2.3444 1-4 EEL = 3.7516 VDWAALS = 39.5767 - EELEC = 58.5488 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 58.5488 EHBOND = 0.0000 RESTRAINT = 0.0152 + EAMBER (non-restraint) = 29.4770 Ewald error estimate: 0.1639E-03 ------------------------------------------------------------------------------ @@ -359,41 +401,41 @@ NGLY -------------------------------------------------------------------------------- |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> -| Read coords time 0.01 ( 0.32% of Total) +| Read coords time 0.01 ( 0.38% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.14 (81.92% of List ) -| Other 0.03 (18.08% of List ) -| List time 0.17 (11.14% of Nonbo) -| Short_ene time 0.95 (98.03% of Direc) -| Other 0.02 ( 1.97% of Direc) -| Direct Ewald time 0.97 (73.69% of Ewald) -| Adjust Ewald time 0.01 ( 0.59% of Ewald) +| Build the list 0.13 (85.90% of List ) +| Other 0.02 (14.10% of List ) +| List time 0.15 (11.96% of Nonbo) +| Short_ene time 0.78 (97.78% of Direc) +| Other 0.02 ( 2.22% of Direc) +| Direct Ewald time 0.80 (72.52% of Ewald) +| Adjust Ewald time 0.01 ( 0.54% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 5.31% of Recip) -| Fill charge grid 0.02 ( 7.21% of Recip) -| Scalar sum 0.11 (36.91% of Recip) -| Grad sum 0.05 (15.02% of Recip) -| FFT back comm time 0.01 (11.50% of FFT t) -| Other 0.09 (88.50% of FFT t) -| FFT time 0.10 (34.73% of Recip) -| Other 0.00 ( 0.81% of Recip) -| Recip Ewald time 0.30 (22.83% of Ewald) -| Force Adjust 0.04 ( 2.70% of Ewald) -| Virial junk 0.00 ( 0.12% of Ewald) +| Fill Bspline coeffs 0.02 ( 7.69% of Recip) +| Fill charge grid 0.02 ( 7.72% of Recip) +| Scalar sum 0.08 (29.18% of Recip) +| Grad sum 0.05 (17.60% of Recip) +| FFT back comm time 0.01 ( 8.93% of FFT t) +| Other 0.10 (91.07% of FFT t) +| FFT time 0.11 (37.42% of Recip) +| Other 0.00 ( 0.38% of Recip) +| Recip Ewald time 0.29 (26.05% of Ewald) +| Force Adjust 0.01 ( 0.67% of Ewald) +| Virial junk 0.00 ( 0.14% of Ewald) | Other 0.00 ( 0.07% of Ewald) -| Ewald time 1.32 (88.85% of Nonbo) -| Nonbond force 1.49 (92.87% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.42% of Force) -| FRC Collect time 0.00 ( 0.15% of Force) -| Other 0.11 ( 6.56% of Force) -| Force time 1.60 (93.85% of Runmd) -| Shake time 0.01 ( 0.50% of Runmd) -| Verlet update time 0.09 ( 5.05% of Runmd) -| CRD distribute time 0.00 ( 0.08% of Runmd) -| Other 0.01 ( 0.52% of Runmd) -| Runmd Time 1.71 (96.40% of Total) -| Other 0.06 ( 3.28% of Total) -| Total time 1.77 (100.0% of ALL ) +| Ewald time 1.10 (88.04% of Nonbo) +| Nonbond force 1.25 (88.94% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.41% of Force) +| FRC Collect time 0.00 ( 0.14% of Force) +| Other 0.15 (10.50% of Force) +| Force time 1.41 (93.62% of Runmd) +| Shake time 0.01 ( 0.35% of Runmd) +| Verlet update time 0.07 ( 4.75% of Runmd) +| CRD distribute time 0.00 ( 0.05% of Runmd) +| Other 0.02 ( 1.22% of Runmd) +| Runmd Time 1.50 (95.94% of Total) +| Other 0.06 ( 3.67% of Total) +| Total time 1.57 (100.0% of ALL ) | Number of list builds : 5 @@ -403,11 +445,11 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 1.71 Per Step(ms) = 34.17 -| ns/day = 5.06 seconds/ns = 17087.11 +| Elapsed(s) = 1.51 Per Step(ms) = 30.11 +| ns/day = 5.74 seconds/ns = 15053.58 | ----------------------------------------------------- -| Job began at 02:46:02.373 on 03/04/2018 -| Setup done at 02:46:02.440 on 03/04/2018 -| Run done at 02:46:04.148 on 03/04/2018 +| Job began at 15:00:14.954 on 09/21/2018 +| Setup done at 15:00:15.018 on 09/21/2018 +| Run done at 15:00:16.524 on 09/21/2018 | wallclock() was called 2783 times diff --git test/nfe/bbmd/save.sander/mdout.2 test/nfe/bbmd/save.sander/mdout.2 index 17ede21187..8119222029 100644 --- test/nfe/bbmd/save.sander/mdout.2 +++ test/nfe/bbmd/save.sander/mdout.2 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/17/2016 at 14:47:35 +| Run on 09/21/2018 at 15:00:14 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/bbmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/bbmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -46,7 +46,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &bbmd @@ -89,8 +89,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -161,13 +161,13 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS @@ -242,109 +242,150 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 651498 +| Local SIZE OF NONBOND LIST = 331663 | TOTAL SIZE OF NONBOND LIST = 651498 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 295.95 PRESS = 0.0 - Etot = -8385.6493 EKtot = 1871.6599 EPtot = -10257.3092 + Etot = -8385.6453 EKtot = 1871.6599 EPtot = -10257.3053 BOND = 21.9397 ANGLE = 68.0282 DIHED = 69.2900 1-4 NB = 32.7028 1-4 EEL = 521.1337 VDWAALS = 1390.4611 - EELEC = -12360.8648 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12360.8648 EHBOND = 0.0000 RESTRAINT = 0.0040 + EAMBER (non-restraint) = -10257.3092 Ewald error estimate: 0.2388E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.004 STSM : 0.000 +=============================================================================== NFE : BBMD : exchanged coordinates/velocities with 1 at t = 0.012 NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 295.39 PRESS = 0.0 - Etot = -8437.2326 EKtot = 1868.1444 EPtot = -10305.3770 + Etot = -8437.2296 EKtot = 1868.1444 EPtot = -10305.3740 BOND = 24.7287 ANGLE = 67.6278 DIHED = 72.4038 1-4 NB = 34.0088 1-4 EEL = 541.6417 VDWAALS = 1316.1134 - EELEC = -12361.9012 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12361.9012 EHBOND = 0.0000 RESTRAINT = 0.0030 + EAMBER (non-restraint) = -10305.3770 Ewald error estimate: 0.3189E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.003 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 287.81 PRESS = 0.0 - Etot = -8425.2272 EKtot = 1820.1993 EPtot = -10245.4265 + Etot = -8425.2192 EKtot = 1820.1993 EPtot = -10245.4186 BOND = 24.7555 ANGLE = 66.7336 DIHED = 75.7431 1-4 NB = 31.4573 1-4 EEL = 535.2650 VDWAALS = 1341.8806 - EELEC = -12321.2616 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12321.2616 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10245.4265 Ewald error estimate: 0.1311E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.008 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 290.53 PRESS = 0.0 - Etot = -8414.7643 EKtot = 1837.3792 EPtot = -10252.1434 + Etot = -8414.7515 EKtot = 1837.3792 EPtot = -10252.1307 BOND = 31.8822 ANGLE = 66.9354 DIHED = 72.3486 1-4 NB = 28.3903 1-4 EEL = 536.6156 VDWAALS = 1368.5498 - EELEC = -12356.8653 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12356.8653 EHBOND = 0.0000 RESTRAINT = 0.0127 + EAMBER (non-restraint) = -10252.1434 Ewald error estimate: 0.4225E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.013 STSM : 0.000 +=============================================================================== NFE : BBMD : exchanged coordinates/velocities with 1 at t = 0.048 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 298.37 PRESS = 0.0 - Etot = -8407.7378 EKtot = 1886.9704 EPtot = -10294.7081 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 303.27 PRESS = 0.0 + Etot = -8376.7226 EKtot = 1917.9797 EPtot = -10294.7023 BOND = 25.1869 ANGLE = 70.1428 DIHED = 73.3947 1-4 NB = 29.7521 1-4 EEL = 526.8671 VDWAALS = 1404.3744 - EELEC = -12424.4262 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12424.4262 EHBOND = 0.0000 RESTRAINT = 0.0058 + EAMBER (non-restraint) = -10294.7081 Ewald error estimate: 0.1906E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.006 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 300.76 PRESS = 0.0 - Etot = -8357.0473 EKtot = 1902.0540 EPtot = -10259.1013 + Etot = -8357.0365 EKtot = 1902.0540 EPtot = -10259.0904 BOND = 38.6101 ANGLE = 77.0064 DIHED = 70.2016 1-4 NB = 28.7337 1-4 EEL = 523.5960 VDWAALS = 1438.3613 - EELEC = -12435.6103 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12435.6103 EHBOND = 0.0000 RESTRAINT = 0.0108 + EAMBER (non-restraint) = -10259.1013 Ewald error estimate: 0.2776E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.011 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 283.94 PRESS = 0.0 - Etot = -8351.3316 EKtot = 1795.6965 EPtot = -10147.0281 + Etot = -8351.3158 EKtot = 1795.6965 EPtot = -10147.0123 BOND = 35.5766 ANGLE = 79.2020 DIHED = 72.2858 1-4 NB = 28.4389 1-4 EEL = 525.6522 VDWAALS = 1458.1718 - EELEC = -12346.3554 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12346.3554 EHBOND = 0.0000 RESTRAINT = 0.0158 + EAMBER (non-restraint) = -10147.0281 Ewald error estimate: 0.1502E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.016 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 295.65 PRESS = 0.0 - Etot = -8338.6021 EKtot = 1869.7395 EPtot = -10208.3416 + Etot = -8338.5813 EKtot = 1869.7395 EPtot = -10208.3208 BOND = 38.9256 ANGLE = 74.6408 DIHED = 66.8360 1-4 NB = 29.2024 1-4 EEL = 519.8959 VDWAALS = 1447.5088 - EELEC = -12385.3511 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12385.3511 EHBOND = 0.0000 RESTRAINT = 0.0208 + EAMBER (non-restraint) = -10208.3416 Ewald error estimate: 0.2125E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.021 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 296.94 PRESS = 0.0 - Etot = -8337.1100 EKtot = 1877.9218 EPtot = -10215.0318 + Etot = -8337.0843 EKtot = 1877.9218 EPtot = -10215.0061 BOND = 30.0024 ANGLE = 78.2499 DIHED = 74.7666 1-4 NB = 28.1633 1-4 EEL = 516.0142 VDWAALS = 1425.5160 - EELEC = -12367.7441 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12367.7441 EHBOND = 0.0000 RESTRAINT = 0.0257 + EAMBER (non-restraint) = -10215.0318 Ewald error estimate: 0.1402E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.026 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.35 PRESS = 0.0 - Etot = -8326.1136 EKtot = 1905.7867 EPtot = -10231.9002 + Etot = -8326.0828 EKtot = 1905.7867 EPtot = -10231.8695 BOND = 31.7526 ANGLE = 62.2943 DIHED = 75.8211 1-4 NB = 29.9488 1-4 EEL = 515.8391 VDWAALS = 1400.7594 - EELEC = -12348.3156 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12348.3156 EHBOND = 0.0000 RESTRAINT = 0.0308 + EAMBER (non-restraint) = -10231.9002 Ewald error estimate: 0.5180E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.031 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 50 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 295.56 PRESS = 0.0 - Etot = -8386.0165 EKtot = 1869.2078 EPtot = -10255.2243 + Etot = -8385.9940 EKtot = 1869.2145 EPtot = -10255.2085 BOND = 29.4815 ANGLE = 72.4345 DIHED = 70.3595 1-4 NB = 29.9298 1-4 EEL = 521.7461 VDWAALS = 1407.1182 - EELEC = -12386.2939 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12386.2939 EHBOND = 0.0000 RESTRAINT = 0.0158 + EAMBER (non-restraint) = -10255.2243 Ewald error estimate: 0.1681E-03 ------------------------------------------------------------------------------ @@ -352,11 +393,12 @@ NGLY R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 4.96 PRESS = 0.0 - Etot = 44.5072 EKtot = 31.3739 EPtot = 52.3651 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 5.06 PRESS = 0.0 + Etot = 45.0203 EKtot = 32.0318 EPtot = 52.3668 BOND = 5.1497 ANGLE = 4.4115 DIHED = 3.3129 1-4 NB = 1.4793 1-4 EEL = 3.7357 VDWAALS = 32.2456 - EELEC = 32.4833 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 32.4833 EHBOND = 0.0000 RESTRAINT = 0.0096 + EAMBER (non-restraint) = 52.3573 Ewald error estimate: 0.7987E-04 ------------------------------------------------------------------------------ @@ -365,51 +407,56 @@ NGLY 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.34% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.35% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.29 (90.92% of List ) -| Other 0.03 ( 9.08% of List ) -| List time 0.32 (11.60% of Nonbo) -| Short_ene time 1.84 (99.12% of Direc) -| Other 0.02 ( 0.88% of Direc) -| Direct Ewald time 1.85 (76.69% of Ewald) -| Adjust Ewald time 0.01 ( 0.61% of Ewald) +| Build the list 0.14 (87.04% of List ) +| Other 0.02 (12.96% of List ) +| List time 0.16 (12.54% of Nonbo) +| Short_ene time 0.79 (97.85% of Direc) +| Other 0.02 ( 2.15% of Direc) +| Direct Ewald time 0.81 (70.76% of Ewald) +| Adjust Ewald time 0.01 ( 0.51% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 4.15% of Recip) -| Fill charge grid 0.04 ( 7.39% of Recip) -| Scalar sum 0.22 (40.97% of Recip) -| Grad sum 0.09 (16.16% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.17 (100.0% of FFT t) -| FFT time 0.17 (31.30% of Recip) -| Other 0.00 ( 0.03% of Recip) -| Recip Ewald time 0.54 (22.55% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.05% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 2.42 (88.40% of Nonbo) -| Nonbond force 2.73 (91.68% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.42% of Force) -| Other 0.24 ( 7.90% of Force) -| Force time 2.98 (96.37% of Runmd) -| Shake time 0.02 ( 0.54% of Runmd) -| Verlet update time 0.09 ( 2.90% of Runmd) -| Other 0.01 ( 0.19% of Runmd) -| Runmd Time 3.09 (97.96% of Total) -| Other 0.05 ( 1.69% of Total) -| Total time 3.16 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Fill Bspline coeffs 0.02 ( 7.47% of Recip) +| Fill charge grid 0.02 ( 7.68% of Recip) +| Scalar sum 0.08 (28.58% of Recip) +| Grad sum 0.05 (17.87% of Recip) +| FFT back comm time 0.01 ( 9.63% of FFT t) +| Other 0.10 (90.37% of FFT t) +| FFT time 0.11 (37.89% of Recip) +| Other 0.00 ( 0.50% of Recip) +| Recip Ewald time 0.29 (25.11% of Ewald) +| Force Adjust 0.04 ( 3.40% of Ewald) +| Virial junk 0.00 ( 0.14% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.15 (87.45% of Nonbo) +| Nonbond force 1.31 (92.70% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.40% of Force) +| FRC Collect time 0.00 ( 0.14% of Force) +| Other 0.10 ( 6.75% of Force) +| Force time 1.42 (94.06% of Runmd) +| Shake time 0.01 ( 0.37% of Runmd) +| Verlet update time 0.07 ( 4.74% of Runmd) +| CRD distribute time 0.00 ( 0.05% of Runmd) +| Other 0.01 ( 0.78% of Runmd) +| Runmd Time 1.51 (95.95% of Total) +| Other 0.06 ( 3.70% of Total) +| Total time 1.57 (100.0% of ALL ) + +| Number of list builds : 5 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 3.09 Per Step(ms) = 61.89 -| ns/day = 2.79 seconds/ns = 30946.83 +| Elapsed(s) = 1.51 Per Step(ms) = 30.11 +| ns/day = 5.74 seconds/ns = 15055.72 | ----------------------------------------------------- -| Job began at 14:47:35.839 on 06/17/2016 -| Setup done at 14:47:35.905 on 06/17/2016 -| Run done at 14:47:38.999 on 06/17/2016 -| wallclock() was called 2683 times +| Job began at 15:00:14.954 on 09/21/2018 +| Setup done at 15:00:15.018 on 09/21/2018 +| Run done at 15:00:16.524 on 09/21/2018 +| wallclock() was called 2783 times diff --git test/nfe/bbmd/save.sander/mdout.3 test/nfe/bbmd/save.sander/mdout.3 index f6836b5d48..aab32a8a91 100644 --- test/nfe/bbmd/save.sander/mdout.3 +++ test/nfe/bbmd/save.sander/mdout.3 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/17/2016 at 14:47:35 +| Run on 09/21/2018 at 15:00:14 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/bbmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/bbmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -46,7 +46,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &bbmd @@ -90,8 +90,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -162,13 +162,13 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS @@ -238,109 +238,150 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 651110 +| Local SIZE OF NONBOND LIST = 330481 | TOTAL SIZE OF NONBOND LIST = 651110 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 298.88 PRESS = 0.0 - Etot = -8242.6824 EKtot = 1890.2031 EPtot = -10132.8855 + Etot = -8242.6798 EKtot = 1890.2031 EPtot = -10132.8829 BOND = 35.8714 ANGLE = 58.9761 DIHED = 71.9607 1-4 NB = 30.1761 1-4 EEL = 529.0867 VDWAALS = 1322.1277 - EELEC = -12181.0842 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12181.0842 EHBOND = 0.0000 RESTRAINT = 0.0026 + EAMBER (non-restraint) = -10132.8855 Ewald error estimate: 0.3336E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.003 STSM : 0.000 +=============================================================================== NFE : BBMD : exchanged coordinates/velocities with 4 at t = 0.012 NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 321.58 PRESS = 0.0 - Etot = -8063.9827 EKtot = 2033.7779 EPtot = -10097.7606 + Etot = -8063.9808 EKtot = 2033.7779 EPtot = -10097.7587 BOND = 26.7320 ANGLE = 68.3762 DIHED = 76.8229 1-4 NB = 30.3875 1-4 EEL = 538.8947 VDWAALS = 1421.5697 - EELEC = -12260.5436 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12260.5436 EHBOND = 0.0000 RESTRAINT = 0.0020 + EAMBER (non-restraint) = -10097.7606 Ewald error estimate: 0.1519E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.002 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 321.40 PRESS = 0.0 - Etot = -8072.1500 EKtot = 2032.5954 EPtot = -10104.7454 + Etot = -8072.1457 EKtot = 2032.5954 EPtot = -10104.7411 BOND = 35.9385 ANGLE = 58.1162 DIHED = 81.0251 1-4 NB = 30.6838 1-4 EEL = 543.7134 VDWAALS = 1443.1021 - EELEC = -12297.3246 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12297.3246 EHBOND = 0.0000 RESTRAINT = 0.0043 + EAMBER (non-restraint) = -10104.7454 Ewald error estimate: 0.1799E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.004 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 315.45 PRESS = 0.0 - Etot = -8086.6028 EKtot = 1994.9816 EPtot = -10081.5844 + Etot = -8086.5961 EKtot = 1994.9816 EPtot = -10081.5777 BOND = 28.8891 ANGLE = 57.5939 DIHED = 80.3435 1-4 NB = 34.8315 1-4 EEL = 539.7066 VDWAALS = 1449.0863 - EELEC = -12272.0353 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12272.0353 EHBOND = 0.0000 RESTRAINT = 0.0067 + EAMBER (non-restraint) = -10081.5844 Ewald error estimate: 0.1132E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.007 STSM : 0.000 +=============================================================================== NFE : BBMD : exchanged coordinates/velocities with 4 at t = 0.048 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 305.29 PRESS = 0.0 - Etot = -8174.9927 EKtot = 1930.7392 EPtot = -10105.7319 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 300.61 PRESS = 0.0 + Etot = -8204.5870 EKtot = 1901.1429 EPtot = -10105.7299 BOND = 31.7513 ANGLE = 62.7226 DIHED = 72.8048 1-4 NB = 34.0860 1-4 EEL = 528.8663 VDWAALS = 1316.1854 - EELEC = -12152.1483 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12152.1483 EHBOND = 0.0000 RESTRAINT = 0.0021 + EAMBER (non-restraint) = -10105.7319 Ewald error estimate: 0.2713E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.002 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 297.47 PRESS = 0.0 - Etot = -8193.1386 EKtot = 1881.2533 EPtot = -10074.3919 + Etot = -8193.1320 EKtot = 1881.2533 EPtot = -10074.3853 BOND = 36.2983 ANGLE = 62.7250 DIHED = 74.7227 1-4 NB = 34.5427 1-4 EEL = 530.9186 VDWAALS = 1320.2574 - EELEC = -12133.8565 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12133.8565 EHBOND = 0.0000 RESTRAINT = 0.0065 + EAMBER (non-restraint) = -10074.3919 Ewald error estimate: 0.2750E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.007 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 299.71 PRESS = 0.0 - Etot = -8188.1130 EKtot = 1895.4631 EPtot = -10083.5761 + Etot = -8188.1042 EKtot = 1895.4631 EPtot = -10083.5672 BOND = 33.2541 ANGLE = 61.1173 DIHED = 73.0462 1-4 NB = 33.7396 1-4 EEL = 528.2327 VDWAALS = 1317.2511 - EELEC = -12130.2170 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12130.2170 EHBOND = 0.0000 RESTRAINT = 0.0088 + EAMBER (non-restraint) = -10083.5761 Ewald error estimate: 0.2557E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.009 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.18 PRESS = 0.0 - Etot = -8189.0628 EKtot = 1898.4208 EPtot = -10087.4836 + Etot = -8189.0498 EKtot = 1898.4208 EPtot = -10087.4707 BOND = 25.0920 ANGLE = 57.1845 DIHED = 70.5873 1-4 NB = 32.8330 1-4 EEL = 537.5637 VDWAALS = 1318.6690 - EELEC = -12129.4132 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12129.4132 EHBOND = 0.0000 RESTRAINT = 0.0129 + EAMBER (non-restraint) = -10087.4836 Ewald error estimate: 0.4178E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.013 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 304.07 PRESS = 0.0 - Etot = -8182.0458 EKtot = 1923.0347 EPtot = -10105.0805 + Etot = -8182.0304 EKtot = 1923.0347 EPtot = -10105.0651 BOND = 35.0105 ANGLE = 64.0850 DIHED = 77.2842 1-4 NB = 31.6637 1-4 EEL = 539.1901 VDWAALS = 1315.4739 - EELEC = -12167.7879 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12167.7879 EHBOND = 0.0000 RESTRAINT = 0.0154 + EAMBER (non-restraint) = -10105.0805 Ewald error estimate: 0.3432E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.015 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 307.41 PRESS = 0.0 - Etot = -8172.9469 EKtot = 1944.1342 EPtot = -10117.0810 + Etot = -8172.9281 EKtot = 1944.1342 EPtot = -10117.0623 BOND = 24.3915 ANGLE = 71.1044 DIHED = 73.6601 1-4 NB = 36.4353 1-4 EEL = 529.0825 VDWAALS = 1305.5854 - EELEC = -12157.3403 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12157.3403 EHBOND = 0.0000 RESTRAINT = 0.0188 + EAMBER (non-restraint) = -10117.0810 Ewald error estimate: 0.7498E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.019 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 50 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 303.89 PRESS = 0.0 - Etot = -8186.0263 EKtot = 1921.8638 EPtot = -10107.8901 + Etot = -8186.0200 EKtot = 1921.8642 EPtot = -10107.8843 BOND = 30.7561 ANGLE = 60.6466 DIHED = 73.1581 1-4 NB = 32.5927 1-4 EEL = 530.0608 VDWAALS = 1318.0068 - EELEC = -12153.1112 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12153.1112 EHBOND = 0.0000 RESTRAINT = 0.0058 + EAMBER (non-restraint) = -10107.8901 Ewald error estimate: 0.2257E-03 ------------------------------------------------------------------------------ @@ -348,11 +389,12 @@ NGLY R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 4.35 PRESS = 0.0 - Etot = 26.8246 EKtot = 27.4919 EPtot = 26.1878 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 4.41 PRESS = 0.0 + Etot = 26.8096 EKtot = 27.9194 EPtot = 26.1897 BOND = 3.9574 ANGLE = 5.5976 DIHED = 2.2614 1-4 NB = 1.8859 1-4 EEL = 4.6175 VDWAALS = 4.7574 - EELEC = 26.0520 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 26.0520 EHBOND = 0.0000 RESTRAINT = 0.0063 + EAMBER (non-restraint) = 26.1834 Ewald error estimate: 0.1174E-03 ------------------------------------------------------------------------------ @@ -361,51 +403,56 @@ NGLY 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.35% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.38% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.29 (91.00% of List ) -| Other 0.03 ( 9.00% of List ) -| List time 0.32 (11.70% of Nonbo) -| Short_ene time 1.83 (99.10% of Direc) -| Other 0.02 ( 0.90% of Direc) -| Direct Ewald time 1.85 (76.59% of Ewald) -| Adjust Ewald time 0.01 ( 0.61% of Ewald) +| Build the list 0.13 (85.83% of List ) +| Other 0.02 (14.17% of List ) +| List time 0.15 (11.95% of Nonbo) +| Short_ene time 0.78 (97.77% of Direc) +| Other 0.02 ( 2.23% of Direc) +| Direct Ewald time 0.80 (72.67% of Ewald) +| Adjust Ewald time 0.01 ( 0.53% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 4.10% of Recip) -| Fill charge grid 0.04 ( 7.38% of Recip) -| Scalar sum 0.22 (40.80% of Recip) -| Grad sum 0.09 (16.64% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.17 (100.0% of FFT t) -| FFT time 0.17 (31.04% of Recip) -| Other 0.00 ( 0.03% of Recip) -| Recip Ewald time 0.55 (22.64% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.05% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 2.41 (88.30% of Nonbo) -| Nonbond force 2.73 (99.32% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.46% of Force) -| Other 0.01 ( 0.21% of Force) -| Force time 2.75 (88.80% of Runmd) -| Shake time 0.02 ( 0.54% of Runmd) -| Verlet update time 0.09 ( 2.88% of Runmd) -| Other 0.24 ( 7.79% of Runmd) -| Runmd Time 3.10 (98.02% of Total) -| Other 0.05 ( 1.63% of Total) -| Total time 3.16 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Fill Bspline coeffs 0.02 ( 7.51% of Recip) +| Fill charge grid 0.02 ( 7.73% of Recip) +| Scalar sum 0.08 (28.95% of Recip) +| Grad sum 0.05 (17.72% of Recip) +| FFT back comm time 0.01 ( 8.89% of FFT t) +| Other 0.10 (91.11% of FFT t) +| FFT time 0.11 (37.78% of Recip) +| Other 0.00 ( 0.30% of Recip) +| Recip Ewald time 0.29 (25.93% of Ewald) +| Force Adjust 0.01 ( 0.66% of Ewald) +| Virial junk 0.00 ( 0.14% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.10 (88.04% of Nonbo) +| Nonbond force 1.25 (92.85% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.43% of Force) +| FRC Collect time 0.00 ( 0.15% of Force) +| Other 0.09 ( 6.57% of Force) +| Force time 1.35 (89.66% of Runmd) +| Shake time 0.01 ( 0.36% of Runmd) +| Verlet update time 0.07 ( 4.72% of Runmd) +| CRD distribute time 0.00 ( 0.04% of Runmd) +| Other 0.08 ( 5.22% of Runmd) +| Runmd Time 1.50 (95.94% of Total) +| Other 0.06 ( 3.67% of Total) +| Total time 1.57 (100.0% of ALL ) + +| Number of list builds : 5 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 3.10 Per Step(ms) = 61.95 -| ns/day = 2.79 seconds/ns = 30974.20 +| Elapsed(s) = 1.51 Per Step(ms) = 30.11 +| ns/day = 5.74 seconds/ns = 15053.58 | ----------------------------------------------------- -| Job began at 14:47:35.839 on 06/17/2016 -| Setup done at 14:47:35.903 on 06/17/2016 -| Run done at 14:47:39.000 on 06/17/2016 -| wallclock() was called 2683 times +| Job began at 15:00:14.954 on 09/21/2018 +| Setup done at 15:00:15.018 on 09/21/2018 +| Run done at 15:00:16.524 on 09/21/2018 +| wallclock() was called 2783 times diff --git test/nfe/bbmd/save.sander/mdout.4 test/nfe/bbmd/save.sander/mdout.4 index 8b3a99e338..b251a38dc8 100644 --- test/nfe/bbmd/save.sander/mdout.4 +++ test/nfe/bbmd/save.sander/mdout.4 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/17/2016 at 14:47:35 +| Run on 09/21/2018 at 15:00:14 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/bbmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/bbmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -46,7 +46,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &bbmd @@ -86,8 +86,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -158,13 +158,13 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS @@ -239,7 +239,7 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 650668 +| Local SIZE OF NONBOND LIST = 331029 | TOTAL SIZE OF NONBOND LIST = 650668 NFE : BBMD : exchanged coordinates/velocities with 1 at t = 0.006 @@ -251,6 +251,9 @@ NGLY Ewald error estimate: 0.2510E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NFE : BBMD : exchanged coordinates/velocities with 3 at t = 0.012 NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 311.09 PRESS = 0.0 @@ -261,6 +264,9 @@ NGLY Ewald error estimate: 0.4085E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 305.94 PRESS = 0.0 Etot = -8166.1719 EKtot = 1934.8274 EPtot = -10100.9993 @@ -270,6 +276,9 @@ NGLY Ewald error estimate: 0.1985E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 306.06 PRESS = 0.0 Etot = -8153.1540 EKtot = 1935.6074 EPtot = -10088.7613 @@ -279,16 +288,22 @@ NGLY Ewald error estimate: 0.2068E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NFE : BBMD : exchanged coordinates/velocities with 3 at t = 0.048 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 320.55 PRESS = 0.0 - Etot = -8049.2970 EKtot = 2027.2289 EPtot = -10076.5259 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 325.50 PRESS = 0.0 + Etot = -8017.9689 EKtot = 2058.5570 EPtot = -10076.5259 BOND = 34.3682 ANGLE = 61.6542 DIHED = 82.6050 1-4 NB = 34.4701 1-4 EEL = 540.5039 VDWAALS = 1446.9701 EELEC = -12277.0974 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.5853E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 323.37 PRESS = 0.0 Etot = -8019.2389 EKtot = 2045.0595 EPtot = -10064.2984 @@ -298,6 +313,9 @@ NGLY Ewald error estimate: 0.1821E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 315.08 PRESS = 0.0 Etot = -8015.9971 EKtot = 1992.6155 EPtot = -10008.6126 @@ -307,6 +325,9 @@ NGLY Ewald error estimate: 0.4192E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 318.98 PRESS = 0.0 Etot = -8008.2151 EKtot = 2017.2765 EPtot = -10025.4916 @@ -316,6 +337,9 @@ NGLY Ewald error estimate: 0.2589E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 323.44 PRESS = 0.0 Etot = -8003.8742 EKtot = 2045.5263 EPtot = -10049.4006 @@ -325,6 +349,9 @@ NGLY Ewald error estimate: 0.2399E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 312.82 PRESS = 0.0 Etot = -8003.8014 EKtot = 1978.3197 EPtot = -9982.1212 @@ -334,15 +361,19 @@ NGLY Ewald error estimate: 0.2201E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 50 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 320.00 PRESS = 0.0 - Etot = -8045.2340 EKtot = 2023.7613 EPtot = -10068.9954 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 320.31 PRESS = 0.0 + Etot = -8043.2686 EKtot = 2025.7250 EPtot = -10068.9936 BOND = 31.1785 ANGLE = 63.5380 DIHED = 79.1654 1-4 NB = 33.2160 1-4 EEL = 542.5538 VDWAALS = 1446.4713 - EELEC = -12265.1184 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12265.1184 EHBOND = 0.0000 RESTRAINT = 0.0018 + EAMBER (non-restraint) = -10068.9954 Ewald error estimate: 0.1900E-03 ------------------------------------------------------------------------------ @@ -350,11 +381,12 @@ NGLY R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 6.52 PRESS = 0.0 - Etot = 48.5132 EKtot = 41.2492 EPtot = 39.3802 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 7.04 PRESS = 0.0 + Etot = 48.6236 EKtot = 44.4948 EPtot = 39.3792 BOND = 4.3341 ANGLE = 4.7645 DIHED = 3.8047 1-4 NB = 1.9931 1-4 EEL = 2.8278 VDWAALS = 22.0855 - EELEC = 21.6362 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 21.6362 EHBOND = 0.0000 RESTRAINT = 0.0027 + EAMBER (non-restraint) = 39.3765 Ewald error estimate: 0.9671E-04 ------------------------------------------------------------------------------ @@ -363,51 +395,56 @@ NGLY 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.34% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.38% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.30 (91.24% of List ) -| Other 0.03 ( 8.76% of List ) -| List time 0.33 (12.00% of Nonbo) -| Short_ene time 1.83 (99.10% of Direc) -| Other 0.02 ( 0.90% of Direc) -| Direct Ewald time 1.84 (76.60% of Ewald) -| Adjust Ewald time 0.01 ( 0.61% of Ewald) +| Build the list 0.13 (85.87% of List ) +| Other 0.02 (14.13% of List ) +| List time 0.15 (11.29% of Nonbo) +| Short_ene time 0.79 (97.82% of Direc) +| Other 0.02 ( 2.18% of Direc) +| Direct Ewald time 0.81 (68.94% of Ewald) +| Adjust Ewald time 0.01 ( 0.51% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 4.13% of Recip) -| Fill charge grid 0.04 ( 7.38% of Recip) -| Scalar sum 0.22 (41.00% of Recip) -| Grad sum 0.09 (16.26% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.17 (100.0% of FFT t) -| FFT time 0.17 (31.19% of Recip) -| Other 0.00 ( 0.03% of Recip) -| Recip Ewald time 0.54 (22.64% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.04% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 2.41 (88.00% of Nonbo) -| Nonbond force 2.73 (99.37% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.45% of Force) -| Other 0.00 ( 0.18% of Force) -| Force time 2.75 (88.82% of Runmd) -| Shake time 0.02 ( 0.54% of Runmd) -| Verlet update time 0.09 ( 2.84% of Runmd) -| Other 0.24 ( 7.81% of Runmd) -| Runmd Time 3.10 (98.05% of Total) -| Other 0.05 ( 1.59% of Total) -| Total time 3.16 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Fill Bspline coeffs 0.02 ( 6.30% of Recip) +| Fill charge grid 0.02 ( 6.38% of Recip) +| Scalar sum 0.08 (23.80% of Recip) +| Grad sum 0.05 (14.63% of Recip) +| FFT back comm time 0.01 ( 6.03% of FFT t) +| Other 0.16 (93.97% of FFT t) +| FFT time 0.17 (48.54% of Recip) +| Other 0.00 ( 0.36% of Recip) +| Recip Ewald time 0.35 (29.55% of Ewald) +| Force Adjust 0.01 ( 0.81% of Ewald) +| Virial junk 0.00 ( 0.13% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.18 (88.70% of Nonbo) +| Nonbond force 1.33 (98.48% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.43% of Force) +| FRC Collect time 0.00 ( 0.16% of Force) +| Other 0.01 ( 0.94% of Force) +| Force time 1.35 (89.53% of Runmd) +| Shake time 0.01 ( 0.35% of Runmd) +| Verlet update time 0.07 ( 4.70% of Runmd) +| CRD distribute time 0.00 ( 0.05% of Runmd) +| Other 0.08 ( 5.37% of Runmd) +| Runmd Time 1.50 (95.95% of Total) +| Other 0.06 ( 3.67% of Total) +| Total time 1.57 (100.0% of ALL ) + +| Number of list builds : 5 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 3.10 Per Step(ms) = 61.97 -| ns/day = 2.79 seconds/ns = 30983.94 +| Elapsed(s) = 1.51 Per Step(ms) = 30.11 +| ns/day = 5.74 seconds/ns = 15057.16 | ----------------------------------------------------- -| Job began at 14:47:35.840 on 06/17/2016 -| Setup done at 14:47:35.902 on 06/17/2016 -| Run done at 14:47:39.000 on 06/17/2016 -| wallclock() was called 2683 times +| Job began at 15:00:14.954 on 09/21/2018 +| Setup done at 15:00:15.018 on 09/21/2018 +| Run done at 15:00:16.524 on 09/21/2018 +| wallclock() was called 2783 times diff --git test/nfe/common.sh test/nfe/common.sh index 04a37b24e3..4950f8ef78 100644 --- test/nfe/common.sh +++ test/nfe/common.sh @@ -57,24 +57,26 @@ set_SANDER_CMD() NUMPROCS_is_okay="not so much" - X2=$(($1+$1)) - X4=$((X2+X2)) - X8=$((X4+X4)) - X16=$((X8+X8)) - X32=$((X16+X16)) - X64=$((X32+X32)) - - for x in $1 $X2 $X4 $X8 $X16 $X32 $X64; do - if test "${NUMPROCS}" -eq "$x"; then - NUMPROCS_is_okay="yes it is" - break - fi - done + if (( ${NUMPROCS} % $1 == 0 )); then + NUMPROCS_is_okay="yes it is" + break + fi + + if [[ $SANDER = *"sander"* ]]; then + MX=$1 + elif [[ $SANDER = *"pmemd"* ]]; then + MX=$(($1+$1)) + fi + + if (( ${NUMPROCS} < $MX )); then + NUMPROCS_is_okay="not enough" + break + fi if test "${NUMPROCS_is_okay}" != "yes it is" ; then - echo " This test case (`pwd`) requires a least $1 mpi threads." + echo " This test case (`pwd`) requires a least $MX mpi threads." echo " The number of mpi threads must also be a multiple of $1" - echo " and not more than ${X64}. Not running test, exiting ....." + echo " and not more than `expr $1 \* 64`. Not running test, exiting ....." exit 1 fi fi diff --git test/nfe/mwabmd/mdin.1 test/nfe/mwabmd/mdin.1 index 314da6203c..ce77b4495a 100644 --- test/nfe/mwabmd/mdin.1 +++ test/nfe/mwabmd/mdin.1 @@ -16,7 +16,7 @@ umbrella_file = 'umbrella.1.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.1.nc' diff --git test/nfe/mwabmd/mdin.2 test/nfe/mwabmd/mdin.2 index b2d528e5a2..234c2c0de7 100644 --- test/nfe/mwabmd/mdin.2 +++ test/nfe/mwabmd/mdin.2 @@ -16,7 +16,7 @@ umbrella_file = 'umbrella.2.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.2.nc' diff --git test/nfe/mwabmd/mdin.3 test/nfe/mwabmd/mdin.3 index 7c6955c70b..d2d5896751 100644 --- test/nfe/mwabmd/mdin.3 +++ test/nfe/mwabmd/mdin.3 @@ -16,7 +16,7 @@ umbrella_file = 'umbrella.3.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.3.nc' diff --git test/nfe/mwabmd/mdin.4 test/nfe/mwabmd/mdin.4 index b43c550dfd..84d8bdcaee 100644 --- test/nfe/mwabmd/mdin.4 +++ test/nfe/mwabmd/mdin.4 @@ -16,7 +16,7 @@ umbrella_file = 'umbrella.4.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.4.nc' diff --git test/nfe/mwabmd/run-pmemd.sh test/nfe/mwabmd/run-pmemd.sh index 7067d2277f..90b478083c 100755 --- test/nfe/mwabmd/run-pmemd.sh +++ test/nfe/mwabmd/run-pmemd.sh @@ -17,9 +17,9 @@ if test $? -ne 0; then fi set_SANDER pmemd.MPI -set_SANDER_CMD_FIX 8 +set_SANDER_CMD 4 -JUNK="umbrella.?.nc mdout.? restrt.? abmd.?.txt inpcrd.? wt_umbrella.?.nc" +JUNK="umbrella.?.nc mdout.? restrt.? abmd.?.txt inpcrd.? wt_umbrella.?.nc *.ncdump" JUNK="${JUNK} mdcrd.? groups prmtop sander.out *.log logfile.*" # @@ -46,15 +46,13 @@ for i in 1 2 3 4; do done for i in 1 2 3 4; do - do_ncdump '%14.10f' save.pmemd/umbrella.$i.nc umbrella.$i.save.ncdump do_ncdump '%14.10f' umbrella.$i.nc umbrella.$i.ncdump - ../../dacdif umbrella.$i.save.ncdump umbrella.$i.ncdump + ../../dacdif save.pmemd/umbrella.$i.ncdump umbrella.$i.ncdump done for i in 1 2 3 4; do - do_ncdump '%14.10f' save.pmemd/wt_umbrella.$i.nc wt_umbrella.$i.save.ncdump do_ncdump '%14.10f' wt_umbrella.$i.nc wt_umbrella.$i.ncdump - ../../dacdif wt_umbrella.$i.save.ncdump wt_umbrella.$i.ncdump + ../../dacdif save.pmemd/wt_umbrella.$i.ncdump wt_umbrella.$i.ncdump done # @@ -67,4 +65,4 @@ save_junk_on_failure ${JUNK} # remove the junk # -/bin/rm -f ${JUNK} *.ncdump profile_mpi +/bin/rm -f ${JUNK} profile_mpi diff --git test/nfe/mwabmd/run-sander.sh test/nfe/mwabmd/run-sander.sh index fcb4f9df0b..1f3eb7b197 100755 --- test/nfe/mwabmd/run-sander.sh +++ test/nfe/mwabmd/run-sander.sh @@ -17,9 +17,9 @@ if test $? -ne 0; then fi set_SANDER sander.MPI -set_SANDER_CMD_FIX 8 +set_SANDER_CMD 4 -JUNK="umbrella.?.nc mdout.? restrt.? abmd.?.txt inpcrd.? wt_umbrella.?.nc" +JUNK="umbrella.?.nc mdout.? restrt.? abmd.?.txt inpcrd.? wt_umbrella.?.nc *.ncdump" JUNK="${JUNK} mdcrd.? groups prmtop sander.out *.log" # @@ -46,15 +46,13 @@ for i in 1 2 3 4; do done for i in 1 2 3 4; do - do_ncdump '%14.10f' save.sander/umbrella.$i.nc umbrella.$i.save.ncdump do_ncdump '%14.10f' umbrella.$i.nc umbrella.$i.ncdump - ../../dacdif umbrella.$i.save.ncdump umbrella.$i.ncdump + ../../dacdif save.sander/umbrella.$i.ncdump umbrella.$i.ncdump done for i in 1 2 3 4; do - do_ncdump '%14.10f' save.sander/wt_umbrella.$i.nc wt_umbrella.$i.save.ncdump do_ncdump '%14.10f' wt_umbrella.$i.nc wt_umbrella.$i.ncdump - ../../dacdif wt_umbrella.$i.save.ncdump wt_umbrella.$i.ncdump + ../../dacdif save.sander/wt_umbrella.$i.ncdump wt_umbrella.$i.ncdump done # @@ -67,4 +65,4 @@ save_junk_on_failure ${JUNK} # remove the junk # -/bin/rm -f ${JUNK} *.ncdump profile_mpi +/bin/rm -f ${JUNK} profile_mpi diff --git test/nfe/mwabmd/save.pmemd/abmd.1.txt test/nfe/mwabmd/save.pmemd/abmd.1.txt index 4b0621d2cb..b19cdd2638 100644 --- test/nfe/mwabmd/save.pmemd/abmd.1.txt +++ test/nfe/mwabmd/save.pmemd/abmd.1.txt @@ -12,42 +12,42 @@ 0.0160 6.3420914451 0.0251678631 0.0180 6.3421608025 0.0282217244 0.0200 6.3417450466 0.0312104757 - 0.0220 6.3436008195 0.0344254625 - 0.0240 6.3448124084 0.0375961007 - 0.0260 6.3455409836 0.0407296449 - 0.0280 6.3456770107 0.0438003928 - 0.0300 6.3454554417 0.0468212920 - 0.0320 6.3451049651 0.0498100477 - 0.0340 6.3448765504 0.0527978287 - 0.0360 6.3448532651 0.0557967614 - 0.0380 6.3448440287 0.0587733823 - 0.0400 6.3447710093 0.0617141774 - 0.0420 6.3476469281 0.0652236755 - 0.0440 6.3500254281 0.0686503756 - 0.0460 6.3520858677 0.0720245637 - 0.0480 6.3535934183 0.0752885306 - 0.0500 6.3547794461 0.0784790812 - 0.0520 6.3555872398 0.0815714931 - 0.0540 6.3562214945 0.0846019851 - 0.0560 6.3564515702 0.0875098090 - 0.0580 6.3562380608 0.0902768492 - 0.0600 6.3556021131 0.0929018340 - 0.0620 6.3578111933 0.0962389487 - 0.0640 6.3595486957 0.0994762858 - 0.0660 6.3610067864 0.1026692429 - 0.0680 6.3618759772 0.1057375808 - 0.0700 6.3623525431 0.1087250833 - 0.0720 6.3625650724 0.1116565744 - 0.0740 6.3625415406 0.1145289519 - 0.0760 6.3623086094 0.1173376174 - 0.0780 6.3618340578 0.1200640786 - 0.0800 6.3612326526 0.1227354808 - 0.0820 6.3638556029 0.1264448525 - 0.0840 6.3669637800 0.1303348959 - 0.0860 6.3704066384 0.1343499133 - 0.0880 6.3737944452 0.1383622516 - 0.0900 6.3768156369 0.1422793186 - 0.0920 6.3791752983 0.1460244269 - 0.0940 6.3807693726 0.1495757617 - 0.0960 6.3816948944 0.1529572447 - 0.0980 6.3820706511 0.1561896686 + 0.0220 6.3409539706 0.0361702493 + 0.0240 6.3396818636 0.0409909930 + 0.0260 6.3380508045 0.0456644111 + 0.0280 6.3362885818 0.0502165750 + 0.0300 6.3346747123 0.0546996235 + 0.0320 6.3335283794 0.0592030804 + 0.0340 6.3329405383 0.0637832831 + 0.0360 6.3331347378 0.0685523276 + 0.0380 6.3337403439 0.0734267832 + 0.0400 6.3346081856 0.0783832714 + 0.0420 6.3353872052 0.0855223910 + 0.0440 6.3356516044 0.0924392672 + 0.0460 6.3352652762 0.0990620249 + 0.0480 6.3339976604 0.1052660024 + 0.0500 6.3320781773 0.1111203750 + 0.0520 6.3295860245 0.1166293106 + 0.0540 6.3270094918 0.1220050917 + 0.0560 6.3246049212 0.1273750396 + 0.0580 6.3224770635 0.1328065508 + 0.0600 6.3209593711 0.1384989099 + 0.0620 6.3198223028 0.1457875296 + 0.0640 6.3189435539 0.1532097134 + 0.0660 6.3179362096 0.1605529883 + 0.0680 6.3165101225 0.1676510045 + 0.0700 6.3146987063 0.1745126427 + 0.0720 6.3125703609 0.1811654309 + 0.0740 6.3105094188 0.1878282921 + 0.0760 6.3087251538 0.1946316199 + 0.0780 6.3074898352 0.2017540196 + 0.0800 6.3067147290 0.2091529746 + 0.0820 6.3061912408 0.2167040286 + 0.0840 6.3058928831 0.2243930744 + 0.0860 6.3053444400 0.2319191674 + 0.0880 6.3042509901 0.2390884518 + 0.0900 6.3027144700 0.2459529189 + 0.0920 6.3009358589 0.2526302765 + 0.0940 6.2992254260 0.2593236072 + 0.0960 6.2979413879 0.2662889452 + 0.0980 6.2973169135 0.2737077303 diff --git test/nfe/mwabmd/save.pmemd/abmd.2.txt test/nfe/mwabmd/save.pmemd/abmd.2.txt index 3187ec6c5f..7eb92fb2db 100644 --- test/nfe/mwabmd/save.pmemd/abmd.2.txt +++ test/nfe/mwabmd/save.pmemd/abmd.2.txt @@ -1,28 +1,28 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0020 7.3436195531 0.0019947857 - 0.0060 7.3462553532 0.0059844210 - 0.0100 7.3506175249 0.0099703971 - 0.0140 7.3557487885 0.0139438102 - 0.0180 7.3594474244 0.0179111196 - 0.0220 7.3593428073 0.0219046326 - 0.0260 7.3570529106 0.0259100369 - 0.0300 7.3567992716 0.0299011093 - 0.0340 7.3589095690 0.0338798012 - 0.0380 7.3608905307 0.0378516027 - 0.0420 7.3647284192 0.0417814600 - 0.0460 7.3712554125 0.0455818781 - 0.0500 7.3783009010 0.0492269677 - 0.0540 7.3858359112 0.0526721146 - 0.0580 7.3922064088 0.0560549462 - 0.0620 7.3959803102 0.0596175583 - 0.0660 7.3973201132 0.0634379432 - 0.0700 7.3983458751 0.0672901538 - 0.0740 7.3993770055 0.0711360455 - 0.0780 7.3982843090 0.0752562376 - 0.0820 7.3967931362 0.0794203702 - 0.0860 7.3955313776 0.0835485535 - 0.0900 7.3933353907 0.0877705072 - 0.0940 7.3905660653 0.0920224266 - 0.0980 7.3876406465 0.0962458867 + 0.0000 7.3427665757 0.0000000000 + 0.0040 7.3446895772 0.0039896524 + 0.0080 7.3482807687 0.0079783806 + 0.0120 7.3532386361 0.0119588849 + 0.0160 7.3578770687 0.0159269124 + 0.0200 6.4915905107 0.0296790296 + 0.0240 6.4919906017 0.0436237525 + 0.0280 6.4914538535 0.0576241602 + 0.0320 6.4931911614 0.0712030111 + 0.0360 6.4974584933 0.0841759714 + 0.0400 6.3346081856 0.0783832714 + 0.0440 6.3356516044 0.0924392672 + 0.0480 6.3339976604 0.1052660024 + 0.0520 6.3295860245 0.1166293106 + 0.0560 6.3246049212 0.1273750396 + 0.0600 6.3209593711 0.1384989099 + 0.0640 6.3189435539 0.1532097134 + 0.0680 6.3165101225 0.1676510045 + 0.0720 6.3125703609 0.1811654309 + 0.0760 6.3087251538 0.1946316199 + 0.0800 6.3067147290 0.2091529746 + 0.0840 6.3058928831 0.2243930744 + 0.0880 6.3042509901 0.2390884518 + 0.0920 6.3009358589 0.2526302765 + 0.0960 6.2979413879 0.2662889452 diff --git test/nfe/mwabmd/save.pmemd/abmd.3.txt test/nfe/mwabmd/save.pmemd/abmd.3.txt index ae911a715a..0d6213b9f8 100644 --- test/nfe/mwabmd/save.pmemd/abmd.3.txt +++ test/nfe/mwabmd/save.pmemd/abmd.3.txt @@ -1,19 +1,20 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0040 7.9395458755 0.0039809175 - 0.0100 7.9366475289 0.0099486200 - 0.0160 7.9367675931 0.0159177917 - 0.0220 7.9354763964 0.0218821011 - 0.0280 7.9355332959 0.0278476158 - 0.0340 7.9422845908 0.0337922912 - 0.0400 7.9440168178 0.0397371510 - 0.0460 7.9414040333 0.0457198893 - 0.0520 7.9388529929 0.0516837501 - 0.0580 7.9379608648 0.0576380153 - 0.0640 7.9354016893 0.0635725802 - 0.0700 7.9340142505 0.0695056769 - 0.0760 7.9371127197 0.0754902180 - 0.0820 7.9401457332 0.0814354154 - 0.0880 7.9400135528 0.0873839911 - 0.0940 7.9437032987 0.0932726887 + 0.0000 7.9425702652 0.0000000000 + 0.0060 7.9382950103 0.0059704516 + 0.0120 7.9364275347 0.0119380949 + 0.0180 7.9368124157 0.0179071215 + 0.0240 6.4919906017 0.0436237525 + 0.0300 6.4919880836 0.0644819739 + 0.0360 6.4974584933 0.0841759714 + 0.0420 6.3353872052 0.0855223910 + 0.0480 6.3339976604 0.1052660024 + 0.0540 6.3270094918 0.1220050917 + 0.0600 6.3209593711 0.1384989099 + 0.0660 6.3179362096 0.1605529883 + 0.0720 6.3125703609 0.1811654309 + 0.0780 6.3074898352 0.2017540196 + 0.0840 6.3058928831 0.2243930744 + 0.0900 6.3027144700 0.2459529189 + 0.0960 6.2979413879 0.2662889452 diff --git test/nfe/mwabmd/save.pmemd/abmd.4.txt test/nfe/mwabmd/save.pmemd/abmd.4.txt index ff31c8a689..ab2b5b1cda 100644 --- test/nfe/mwabmd/save.pmemd/abmd.4.txt +++ test/nfe/mwabmd/save.pmemd/abmd.4.txt @@ -1,13 +1,13 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0080 6.4782576403 0.0122506568 - 0.0180 6.4904463792 0.0267730498 - 0.0280 6.4915663521 0.0418068084 - 0.0380 6.5014545512 0.0550981675 - 0.0480 6.5127075825 0.0670806647 - 0.0580 6.5304267866 0.0759484241 - 0.0680 6.5280948212 0.0909108752 - 0.0780 6.5270853051 0.1056890353 - 0.0880 6.5206240037 0.1231954676 - 0.0980 6.5195308780 0.1391442885 + 0.0000 6.4718101196 0.0000000000 + 0.0100 6.4805813972 0.0152386065 + 0.0200 6.4915905107 0.0296790296 + 0.0300 6.4919880836 0.0644819739 + 0.0400 6.5020503277 0.0968500840 + 0.0500 6.5136784005 0.1150166701 + 0.0600 6.3209593711 0.1384989099 + 0.0700 6.3146987063 0.1745126427 + 0.0800 6.3067147290 0.2091529746 + 0.0900 6.3027144700 0.2459529189 diff --git test/nfe/mwabmd/save.pmemd/mdout.1 test/nfe/mwabmd/save.pmemd/mdout.1 index 6c88272f4b..79be53f2e3 100644 --- test/nfe/mwabmd/save.pmemd/mdout.1 +++ test/nfe/mwabmd/save.pmemd/mdout.1 @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 06/06/2016 at 14:46:13 +| Run on 09/06/2018 at 20:58:38 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/mwabmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/mwabmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -37,7 +37,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -48,7 +48,7 @@ File Assignments: umbrella_file = 'umbrella.1.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.1.nc' @@ -62,6 +62,7 @@ File Assignments: / +| irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: @@ -177,7 +178,7 @@ NGLY | Dynamic Memory, Types Used: | Reals 245715 -| Integers 200499 +| Integers 210011 | Nonbonded Pairs Initial Allocation: 358302 @@ -233,150 +234,190 @@ NGLY NFE : selection algorithm parameters: NFE : NFE : selection_freq = 10 (0.0200 ps) - NFE : selection scoring constant = 0.010000 + NFE : selection scoring constant = 0.020000 NFE : selection criterion epsilon = 0.000000 NFE : NFE : () () () () () () () () () () () () () () () () () () () () () () () () NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 310.12 PRESS = 0.0 - Etot = -8188.7886 EKtot = 1961.2513 EPtot = -10150.0400 + Etot = -8188.7760 EKtot = 1961.2513 EPtot = -10150.0274 BOND = 25.3727 ANGLE = 58.6639 DIHED = 80.8338 1-4 NB = 30.8521 1-4 EEL = 539.4401 VDWAALS = 1403.2404 - EELEC = -12288.4429 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12288.4429 EHBOND = 0.0000 RESTRAINT = 0.0126 + EAMBER (non-restraint) = -10150.0400 Ewald error estimate: 0.2391E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.013 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 311.17 PRESS = 0.0 - Etot = -8196.4686 EKtot = 1967.9098 EPtot = -10164.3783 + Etot = -8196.4403 EKtot = 1967.9098 EPtot = -10164.3501 BOND = 25.7998 ANGLE = 67.0917 DIHED = 76.2276 1-4 NB = 30.3557 1-4 EEL = 538.9007 VDWAALS = 1409.3611 - EELEC = -12312.1148 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12312.1148 EHBOND = 0.0000 RESTRAINT = 0.0282 + EAMBER (non-restraint) = -10164.3783 Ewald error estimate: 0.1858E-03 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.020147 / 0.072510 = 0.278 => 1 walker(s) - NFE : selection score for walker 2 is 0.003269 / 0.072510 = 0.045 => 0 walker(s) - NFE : selection score for walker 3 is 0.005663 / 0.072510 = 0.078 => 1 walker(s) - NFE : selection score for walker 4 is 0.043432 / 0.072510 = 0.599 => 2 walker(s) - NFE : Selection entropy 0.384606 is greater than threshold 0.000000 - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 248.61 PRESS = 0.0 - Etot = -8330.3872 EKtot = 1572.2530 EPtot = -9902.6402 - BOND = 39.8411 ANGLE = 60.1336 DIHED = 81.3878 - 1-4 NB = 29.8533 1-4 EEL = 541.7616 VDWAALS = 1525.5343 - EELEC = -12181.1519 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2604E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.028 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.000406 / 0.002335 = 0.174 => 1 walker(s) + NFE : selection score for walker 2 is 0.000011 / 0.002335 = 0.005 => 0 walker(s) + NFE : selection score for walker 3 is 0.000032 / 0.002335 = 0.014 => 0 walker(s) + NFE : selection score for walker 4 is 0.001886 / 0.002335 = 0.808 => 3 walker(s) + NFE : Selection entropy 0.826228 is greater than threshold 0.000000 + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 309.48 PRESS = 0.0 + Etot = -8204.9670 EKtot = 1957.2209 EPtot = -10162.1879 + BOND = 34.4841 ANGLE = 56.5594 DIHED = 80.4516 + 1-4 NB = 30.5678 1-4 EEL = 543.5502 VDWAALS = 1421.4784 + EELEC = -12329.3296 EHBOND = 0.0000 RESTRAINT = 0.0502 + EAMBER (non-restraint) = -10162.2381 + Ewald error estimate: 0.2032E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 274.91 PRESS = 0.0 - Etot = -8331.4747 EKtot = 1738.6204 EPtot = -10070.0952 - BOND = 28.6144 ANGLE = 59.1305 DIHED = 78.1861 - 1-4 NB = 32.4348 1-4 EEL = 538.5957 VDWAALS = 1529.7022 - EELEC = -12336.7588 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2465E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.050 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 304.13 PRESS = 0.0 + Etot = -8219.7331 EKtot = 1923.3656 EPtot = -10143.0986 + BOND = 27.5327 ANGLE = 56.0018 DIHED = 79.6719 + 1-4 NB = 34.6043 1-4 EEL = 539.8766 VDWAALS = 1425.5446 + EELEC = -12306.4039 EHBOND = 0.0000 RESTRAINT = 0.0734 + EAMBER (non-restraint) = -10143.1720 + Ewald error estimate: 0.9427E-04 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.019910 / 0.071750 = 0.277 => 1 walker(s) - NFE : selection score for walker 2 is 0.002711 / 0.071750 = 0.038 => 0 walker(s) - NFE : selection score for walker 3 is 0.005648 / 0.071750 = 0.079 => 1 walker(s) - NFE : selection score for walker 4 is 0.043481 / 0.071750 = 0.606 => 2 walker(s) - NFE : Selection entropy 0.403162 is greater than threshold 0.000000 - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 233.71 PRESS = 0.0 - Etot = -8297.6367 EKtot = 1478.0465 EPtot = -9775.6831 - BOND = 36.1937 ANGLE = 81.5969 DIHED = 83.0992 - 1-4 NB = 31.2332 1-4 EEL = 536.4398 VDWAALS = 1674.8644 - EELEC = -12219.1104 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1195E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.073 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.003264 / 0.004166 = 0.784 => 3 walker(s) + NFE : selection score for walker 2 is 0.000301 / 0.004166 = 0.072 => 1 walker(s) + NFE : selection score for walker 3 is 0.000301 / 0.004166 = 0.072 => 0 walker(s) + NFE : selection score for walker 4 is 0.000301 / 0.004166 = 0.072 => 0 walker(s) + NFE : Selection entropy 0.626047 is greater than threshold 0.000000 + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 304.33 PRESS = 0.0 + Etot = -8214.7597 EKtot = 1924.6797 EPtot = -10139.4394 + BOND = 32.7375 ANGLE = 59.8108 DIHED = 81.8667 + 1-4 NB = 34.3189 1-4 EEL = 540.6806 VDWAALS = 1427.0107 + EELEC = -12315.9698 EHBOND = 0.0000 RESTRAINT = 0.1053 + EAMBER (non-restraint) = -10139.5446 + Ewald error estimate: 0.2810E-04 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 252.27 PRESS = 0.0 - Etot = -8296.8909 EKtot = 1595.4273 EPtot = -9892.3182 - BOND = 29.9652 ANGLE = 79.9020 DIHED = 79.1766 - 1-4 NB = 29.6838 1-4 EEL = 534.0972 VDWAALS = 1674.1583 - EELEC = -12319.3013 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2085E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.105 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 306.17 PRESS = 0.0 + Etot = -8217.6738 EKtot = 1936.3007 EPtot = -10153.9745 + BOND = 27.7620 ANGLE = 67.5250 DIHED = 80.3633 + 1-4 NB = 34.0498 1-4 EEL = 542.3720 VDWAALS = 1444.0653 + EELEC = -12350.2447 EHBOND = 0.0000 RESTRAINT = 0.1328 + EAMBER (non-restraint) = -10154.1073 + Ewald error estimate: 0.1700E-03 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.017977 / 0.094344 = 0.191 => 0 walker(s) - NFE : selection score for walker 2 is 0.002316 / 0.094344 = 0.025 => 1 walker(s) - NFE : selection score for walker 3 is 0.005656 / 0.094344 = 0.060 => 0 walker(s) - NFE : selection score for walker 4 is 0.068395 / 0.094344 = 0.725 => 3 walker(s) - NFE : Selection entropy 0.577510 is greater than threshold 0.000000 - NFE : Selection resampling : new 1 comes from 2 - - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 258.92 PRESS = 0.0 - Etot = -8553.6993 EKtot = 1637.4749 EPtot = -10191.1743 - BOND = 42.1979 ANGLE = 82.7612 DIHED = 79.9809 - 1-4 NB = 28.3505 1-4 EEL = 533.8837 VDWAALS = 1631.1840 - EELEC = -12589.5324 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5996E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.133 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.003278 / 0.011899 = 0.275 => 2 walker(s) + NFE : selection score for walker 2 is 0.003278 / 0.011899 = 0.275 => 1 walker(s) + NFE : selection score for walker 3 is 0.003278 / 0.011899 = 0.275 => 1 walker(s) + NFE : selection score for walker 4 is 0.002066 / 0.011899 = 0.174 => 0 walker(s) + NFE : Selection entropy 0.016849 is greater than threshold 0.000000 + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 298.82 PRESS = 0.0 + Etot = -8216.1590 EKtot = 1889.7927 EPtot = -10105.9517 + BOND = 29.0913 ANGLE = 68.4372 DIHED = 79.1987 + 1-4 NB = 32.9257 1-4 EEL = 547.9543 VDWAALS = 1460.4301 + EELEC = -12324.1567 EHBOND = 0.0000 RESTRAINT = 0.1677 + EAMBER (non-restraint) = -10106.1194 + Ewald error estimate: 0.3806E-03 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 276.86 PRESS = 0.0 - Etot = -8550.6368 EKtot = 1750.9200 EPtot = -10301.5568 - BOND = 36.9550 ANGLE = 79.3555 DIHED = 80.3687 - 1-4 NB = 31.9103 1-4 EEL = 531.5176 VDWAALS = 1560.9379 - EELEC = -12622.6018 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5466E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.168 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 303.32 PRESS = 0.0 + Etot = -8210.6219 EKtot = 1918.2364 EPtot = -10128.8584 + BOND = 33.3262 ANGLE = 62.2842 DIHED = 76.5199 + 1-4 NB = 34.6190 1-4 EEL = 544.8030 VDWAALS = 1451.2291 + EELEC = -12331.8415 EHBOND = 0.0000 RESTRAINT = 0.2018 + EAMBER (non-restraint) = -10129.0601 + Ewald error estimate: 0.2168E-03 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.018790 / 0.104530 = 0.180 => 1 walker(s) - NFE : selection score for walker 2 is 0.004122 / 0.104530 = 0.039 => 0 walker(s) - NFE : selection score for walker 3 is 0.005668 / 0.104530 = 0.054 => 1 walker(s) - NFE : selection score for walker 4 is 0.075950 / 0.104530 = 0.727 => 2 walker(s) - NFE : Selection entropy 0.560194 is greater than threshold 0.000000 - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 216.76 PRESS = 0.0 - Etot = -8778.8978 EKtot = 1370.8419 EPtot = -10149.7397 - BOND = 42.1918 ANGLE = 98.4207 DIHED = 83.6248 - 1-4 NB = 30.9412 1-4 EEL = 536.6392 VDWAALS = 1653.3770 - EELEC = -12594.9344 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3103E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.202 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.001537 / 0.006149 = 0.250 => 1 walker(s) + NFE : selection score for walker 2 is 0.001537 / 0.006149 = 0.250 => 1 walker(s) + NFE : selection score for walker 3 is 0.001537 / 0.006149 = 0.250 => 1 walker(s) + NFE : selection score for walker 4 is 0.001537 / 0.006149 = 0.250 => 1 walker(s) + NFE : Selection entropy 0.000000 is greater than threshold 0.000000 + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 308.05 PRESS = 0.0 + Etot = -8209.3146 EKtot = 1948.2060 EPtot = -10157.5205 + BOND = 33.8149 ANGLE = 59.8723 DIHED = 71.2879 + 1-4 NB = 35.6074 1-4 EEL = 545.7737 VDWAALS = 1439.7417 + EELEC = -12343.8574 EHBOND = 0.0000 RESTRAINT = 0.2391 + EAMBER (non-restraint) = -10157.7596 + Ewald error estimate: 0.1104E-04 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 237.75 PRESS = 0.0 - Etot = -8770.8793 EKtot = 1503.5739 EPtot = -10274.4532 - BOND = 36.6637 ANGLE = 79.3645 DIHED = 74.1602 - 1-4 NB = 31.2130 1-4 EEL = 532.9044 VDWAALS = 1634.1998 - EELEC = -12662.9588 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2986E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.239 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 297.05 PRESS = 0.0 + Etot = -8211.8490 EKtot = 1878.6031 EPtot = -10090.4521 + BOND = 31.0312 ANGLE = 65.2697 DIHED = 73.9875 + 1-4 NB = 31.4588 1-4 EEL = 541.2030 VDWAALS = 1452.8271 + EELEC = -12286.5031 EHBOND = 0.0000 RESTRAINT = 0.2737 + EAMBER (non-restraint) = -10090.7258 + Ewald error estimate: 0.2367E-03 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.016695 / 0.076643 = 0.218 => 1 walker(s) - NFE : selection score for walker 2 is 0.003135 / 0.076643 = 0.041 => 0 walker(s) - NFE : selection score for walker 3 is 0.005617 / 0.076643 = 0.073 => 0 walker(s) - NFE : selection score for walker 4 is 0.051196 / 0.076643 = 0.668 => 3 walker(s) - NFE : Selection entropy 0.462496 is greater than threshold 0.000000 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.274 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.000653 / 0.002614 = 0.250 => 1 walker(s) + NFE : selection score for walker 2 is 0.000653 / 0.002614 = 0.250 => 1 walker(s) + NFE : selection score for walker 3 is 0.000653 / 0.002614 = 0.250 => 1 walker(s) + NFE : selection score for walker 4 is 0.000653 / 0.002614 = 0.250 => 1 walker(s) + NFE : Selection entropy 0.000000 is greater than threshold 0.000000 A V E R A G E S O V E R 10 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 262.11 PRESS = 0.0 - Etot = -8429.5760 EKtot = 1657.6319 EPtot = -10087.2079 - BOND = 34.3795 ANGLE = 74.6421 DIHED = 79.7046 - 1-4 NB = 30.6828 1-4 EEL = 536.4180 VDWAALS = 1569.6559 - EELEC = -12412.6908 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1983E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.26 PRESS = 0.0 + Etot = -8209.0294 EKtot = 1930.5566 EPtot = -10139.5861 + BOND = 30.0952 ANGLE = 62.1516 DIHED = 78.0409 + 1-4 NB = 32.9359 1-4 EEL = 542.4554 VDWAALS = 1433.4928 + EELEC = -12318.8865 EHBOND = 0.0000 RESTRAINT = 0.1285 + EAMBER (non-restraint) = -10139.7145 + Ewald error estimate: 0.1766E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 29.73 PRESS = 0.0 - Etot = 208.6550 EKtot = 188.0206 EPtot = 165.8362 - BOND = 6.1204 ANGLE = 12.3098 DIHED = 2.7736 - 1-4 NB = 1.1175 1-4 EEL = 3.1114 VDWAALS = 96.9319 - EELEC = 173.8696 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8756E-04 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 4.47 PRESS = 0.0 + Etot = 9.3205 EKtot = 28.2698 EPtot = 23.3123 + BOND = 3.2430 ANGLE = 4.4097 DIHED = 3.2446 + 1-4 NB = 1.8627 1-4 EEL = 2.8472 VDWAALS = 18.1987 + EELEC = 20.2416 EHBOND = 0.0000 RESTRAINT = 0.0857 + EAMBER (non-restraint) = 23.2266 + Ewald error estimate: 0.1038E-03 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- @@ -387,73 +428,73 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.06 7.22 -| Nonbond 0.70 77.84 -| Bond 0.00 0.06 -| Angle 0.00 0.17 -| Dihedral 0.00 0.56 -| Shake 0.01 0.90 -| RunMD 0.11 12.48 -| Other 0.01 0.78 +| DataDistrib 0.01 1.15 +| Nonbond 0.40 84.71 +| Bond 0.00 0.00 +| Angle 0.00 0.21 +| Dihedral 0.00 0.52 +| Shake 0.00 0.63 +| RunMD 0.06 12.36 +| Other 0.00 0.42 | ------------------------------ -| Total 0.89 +| Total 0.48 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 -| Build List 0.05 6.04 +| Build List 0.05 10.16 | --------------------------------- -| Total 0.05 6.04 +| Total 0.05 10.16 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.43 48.18 -| Exclude Masked 0.01 0.90 -| Other 0.01 0.78 +| NonBonded Calc 0.23 47.96 +| Exclude Masked 0.00 0.84 +| Other 0.01 1.57 | --------------------------------- -| Total 0.45 49.86 +| Total 0.24 50.37 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.02 1.73 -| Grid Charges 0.02 2.52 -| Scalar Sum 0.03 3.25 -| Gradient Sum 0.03 2.85 -| FFT 0.10 11.53 +| 1D bspline 0.01 2.62 +| Grid Charges 0.01 2.20 +| Scalar Sum 0.02 3.87 +| Gradient Sum 0.01 2.72 +| FFT 0.06 12.67 | --------------------------------- -| Total 0.20 21.88 +| Total 0.11 24.08 | PME Load Balancing CPU Time, Average for All Tasks: | | Routine Sec % | ------------------------------------ | Atom Reassign 0.00 0.00 -| Image Reassign 0.00 0.06 +| Image Reassign 0.00 0.00 | FFT Reassign 0.00 0.00 | ------------------------------------ -| Total 0.00 0.06 +| Total 0.00 0.00 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.80 Per Step(ms) = 17.81 -| ns/day = 9.70 seconds/ns = 8905.60 +| Elapsed(s) = 0.42 Per Step(ms) = 9.41 +| ns/day = 18.36 seconds/ns = 4705.87 | | Average timings for all steps: -| Elapsed(s) = 0.90 Per Step(ms) = 17.96 -| ns/day = 9.62 seconds/ns = 8979.04 +| Elapsed(s) = 0.48 Per Step(ms) = 9.57 +| ns/day = 18.05 seconds/ns = 4786.96 | ----------------------------------------------------- -| Master Setup CPU time: 0.08 seconds -| Master NonSetup CPU time: 0.89 seconds -| Master Total CPU time: 0.98 seconds 0.00 hours +| Master Setup CPU time: 0.05 seconds +| Master NonSetup CPU time: 0.48 seconds +| Master Total CPU time: 0.53 seconds 0.00 hours | Master Setup wall time: 0 seconds -| Master NonSetup wall time: 1 seconds -| Master Total wall time: 1 seconds 0.00 hours +| Master NonSetup wall time: 0 seconds +| Master Total wall time: 0 seconds 0.00 hours diff --git test/nfe/mwabmd/save.pmemd/mdout.2 test/nfe/mwabmd/save.pmemd/mdout.2 index 876ba820f5..8b3f21f16c 100644 --- test/nfe/mwabmd/save.pmemd/mdout.2 +++ test/nfe/mwabmd/save.pmemd/mdout.2 @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 06/06/2016 at 14:46:13 +| Run on 09/06/2018 at 20:58:38 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/mwabmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/mwabmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -37,7 +37,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -48,7 +48,7 @@ File Assignments: umbrella_file = 'umbrella.2.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.2.nc' @@ -62,6 +62,7 @@ File Assignments: / +| irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: @@ -177,7 +178,7 @@ NGLY | Dynamic Memory, Types Used: | Reals 245722 -| Integers 201281 +| Integers 210793 | Nonbonded Pairs Initial Allocation: 358302 @@ -236,133 +237,171 @@ NGLY NFE : selection algorithm parameters: NFE : NFE : selection_freq = 10 (0.0200 ps) - NFE : selection scoring constant = 0.010000 + NFE : selection scoring constant = 0.020000 NFE : selection criterion epsilon = 0.000000 NFE : NFE : () () () () () () () () () () () () () () () () () () () () () () () () NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 295.81 PRESS = 0.0 - Etot = -8386.6443 EKtot = 1870.7978 EPtot = -10257.4421 + Etot = -8386.6363 EKtot = 1870.7978 EPtot = -10257.4341 BOND = 21.9075 ANGLE = 68.0223 DIHED = 69.2843 1-4 NB = 32.7030 1-4 EEL = 521.1360 VDWAALS = 1390.4554 - EELEC = -12360.9506 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12360.9506 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10257.4421 Ewald error estimate: 0.2427E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 304.58 PRESS = 0.0 - Etot = -8388.8308 EKtot = 1926.2407 EPtot = -10315.0715 + Etot = -8388.8129 EKtot = 1926.2407 EPtot = -10315.0536 BOND = 22.6084 ANGLE = 77.7201 DIHED = 67.9834 1-4 NB = 30.4737 1-4 EEL = 521.1888 VDWAALS = 1371.7863 - EELEC = -12406.8323 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12406.8323 EHBOND = 0.0000 RESTRAINT = 0.0179 + EAMBER (non-restraint) = -10315.0715 Ewald error estimate: 0.1019E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 2 comes from 3 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 2 comes from 4 - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 271.54 PRESS = 0.0 - Etot = -8817.0642 EKtot = 1717.2647 EPtot = -10534.3289 - BOND = 26.9736 ANGLE = 80.3920 DIHED = 64.0003 - 1-4 NB = 33.6994 1-4 EEL = 521.7961 VDWAALS = 1367.4899 - EELEC = -12628.6801 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1449E-03 + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 + Etot = -8320.0172 EKtot = 1879.6571 EPtot = -10199.6743 + BOND = 25.7314 ANGLE = 67.7047 DIHED = 76.2864 + 1-4 NB = 31.4941 1-4 EEL = 535.0442 VDWAALS = 1359.5172 + EELEC = -12295.5101 EHBOND = 0.0000 RESTRAINT = 0.0576 + EAMBER (non-restraint) = -10199.7320 + Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 272.97 PRESS = 0.0 - Etot = -8815.0353 EKtot = 1726.3085 EPtot = -10541.3438 - BOND = 28.3407 ANGLE = 66.8605 DIHED = 71.2277 - 1-4 NB = 35.1103 1-4 EEL = 524.5329 VDWAALS = 1381.3823 - EELEC = -12648.7982 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3512E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.058 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 + Etot = -8311.8651 EKtot = 1892.0360 EPtot = -10203.9010 + BOND = 32.8322 ANGLE = 68.2453 DIHED = 72.8983 + 1-4 NB = 28.3884 1-4 EEL = 536.4092 VDWAALS = 1387.0687 + EELEC = -12329.8338 EHBOND = 0.0000 RESTRAINT = 0.0905 + EAMBER (non-restraint) = -10203.9916 + Ewald error estimate: 0.2635E-04 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 2 comes from 3 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.091 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 2 comes from 1 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 261.62 PRESS = 0.0 - Etot = -9046.8712 EKtot = 1654.5544 EPtot = -10701.4256 - BOND = 36.5260 ANGLE = 73.6508 DIHED = 69.3492 - 1-4 NB = 32.5850 1-4 EEL = 523.2579 VDWAALS = 1389.6617 - EELEC = -12826.4562 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3337E-03 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 304.33 PRESS = 0.0 + Etot = -8214.7597 EKtot = 1924.6797 EPtot = -10139.4394 + BOND = 32.7375 ANGLE = 59.8108 DIHED = 81.8667 + 1-4 NB = 34.3189 1-4 EEL = 540.6806 VDWAALS = 1427.0107 + EELEC = -12315.9698 EHBOND = 0.0000 RESTRAINT = 0.1053 + EAMBER (non-restraint) = -10139.5446 + Ewald error estimate: 0.2810E-04 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 247.07 PRESS = 0.0 - Etot = -9027.6555 EKtot = 1562.5482 EPtot = -10590.2038 - BOND = 30.9811 ANGLE = 74.4693 DIHED = 72.5568 - 1-4 NB = 29.0343 1-4 EEL = 517.5794 VDWAALS = 1408.5073 - EELEC = -12723.3320 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2894E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.105 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 306.17 PRESS = 0.0 + Etot = -8217.6738 EKtot = 1936.3007 EPtot = -10153.9745 + BOND = 27.7620 ANGLE = 67.5250 DIHED = 80.3633 + 1-4 NB = 34.0498 1-4 EEL = 542.3720 VDWAALS = 1444.0653 + EELEC = -12350.2447 EHBOND = 0.0000 RESTRAINT = 0.1328 + EAMBER (non-restraint) = -10154.1073 + Ewald error estimate: 0.1700E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 2 comes from 4 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.133 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 2 comes from 1 - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 227.75 PRESS = 0.0 - Etot = -9104.9523 EKtot = 1440.3568 EPtot = -10545.3091 - BOND = 34.2505 ANGLE = 83.4946 DIHED = 65.4999 - 1-4 NB = 29.8400 1-4 EEL = 521.3999 VDWAALS = 1552.3909 - EELEC = -12832.1849 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4257E-03 + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 298.82 PRESS = 0.0 + Etot = -8216.1590 EKtot = 1889.7927 EPtot = -10105.9517 + BOND = 29.0913 ANGLE = 68.4372 DIHED = 79.1987 + 1-4 NB = 32.9257 1-4 EEL = 547.9543 VDWAALS = 1460.4301 + EELEC = -12324.1567 EHBOND = 0.0000 RESTRAINT = 0.1677 + EAMBER (non-restraint) = -10106.1194 + Ewald error estimate: 0.3806E-03 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 218.65 PRESS = 0.0 - Etot = -9090.6597 EKtot = 1382.7772 EPtot = -10473.4369 - BOND = 28.1500 ANGLE = 76.1107 DIHED = 67.8161 - 1-4 NB = 31.8691 1-4 EEL = 521.5694 VDWAALS = 1578.6776 - EELEC = -12777.6297 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2863E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.168 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 303.32 PRESS = 0.0 + Etot = -8210.6219 EKtot = 1918.2364 EPtot = -10128.8584 + BOND = 33.3262 ANGLE = 62.2842 DIHED = 76.5199 + 1-4 NB = 34.6190 1-4 EEL = 544.8030 VDWAALS = 1451.2291 + EELEC = -12331.8415 EHBOND = 0.0000 RESTRAINT = 0.2018 + EAMBER (non-restraint) = -10129.0601 + Ewald error estimate: 0.2168E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 2 comes from 3 - - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 178.76 PRESS = 0.0 - Etot = -9249.4729 EKtot = 1130.5083 EPtot = -10379.9812 - BOND = 31.3239 ANGLE = 91.4511 DIHED = 68.2449 - 1-4 NB = 32.7935 1-4 EEL = 522.3770 VDWAALS = 1733.4868 - EELEC = -12859.6584 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1242E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.202 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 308.05 PRESS = 0.0 + Etot = -8209.3146 EKtot = 1948.2060 EPtot = -10157.5205 + BOND = 33.8149 ANGLE = 59.8723 DIHED = 71.2879 + 1-4 NB = 35.6074 1-4 EEL = 545.7737 VDWAALS = 1439.7417 + EELEC = -12343.8574 EHBOND = 0.0000 RESTRAINT = 0.2391 + EAMBER (non-restraint) = -10157.7596 + Ewald error estimate: 0.1104E-04 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 180.00 PRESS = 0.0 - Etot = -9236.4336 EKtot = 1138.3403 EPtot = -10374.7739 - BOND = 27.6765 ANGLE = 76.3448 DIHED = 66.3415 - 1-4 NB = 32.9938 1-4 EEL = 517.0641 VDWAALS = 1692.3959 - EELEC = -12787.5903 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3192E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.239 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 297.05 PRESS = 0.0 + Etot = -8211.8490 EKtot = 1878.6031 EPtot = -10090.4521 + BOND = 31.0312 ANGLE = 65.2697 DIHED = 73.9875 + 1-4 NB = 31.4588 1-4 EEL = 541.2030 VDWAALS = 1452.8271 + EELEC = -12286.5031 EHBOND = 0.0000 RESTRAINT = 0.2737 + EAMBER (non-restraint) = -10090.7258 + Ewald error estimate: 0.2367E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 2 comes from 4 - + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.274 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 245.87 PRESS = 0.0 - Etot = -8916.3620 EKtot = 1554.9697 EPtot = -10471.3317 - BOND = 28.8738 ANGLE = 76.8516 DIHED = 68.2304 - 1-4 NB = 32.1102 1-4 EEL = 521.1902 VDWAALS = 1486.6234 - EELEC = -12685.2113 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2619E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.45 PRESS = 0.0 + Etot = -8268.7710 EKtot = 1906.4550 EPtot = -10175.2260 + BOND = 29.0843 ANGLE = 66.4892 DIHED = 74.9677 + 1-4 NB = 32.6039 1-4 EEL = 537.6565 VDWAALS = 1418.4132 + EELEC = -12334.5700 EHBOND = 0.0000 RESTRAINT = 0.1294 + EAMBER (non-restraint) = -10175.3554 + Ewald error estimate: 0.1557E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 41.83 PRESS = 0.0 - Etot = 297.9582 EKtot = 264.5363 EPtot = 130.0982 - BOND = 4.3766 ANGLE = 6.8196 DIHED = 2.4334 - 1-4 NB = 1.7522 1-4 EEL = 2.1789 VDWAALS = 133.8997 - EELEC = 167.2186 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1016E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 4.11 PRESS = 0.0 + Etot = 71.5809 EKtot = 25.9753 EPtot = 66.2655 + BOND = 4.2189 ANGLE = 4.9544 DIHED = 4.4567 + 1-4 NB = 2.0755 1-4 EEL = 9.0524 VDWAALS = 35.5252 + EELEC = 32.5117 EHBOND = 0.0000 RESTRAINT = 0.0860 + EAMBER (non-restraint) = 66.1795 + Ewald error estimate: 0.1121E-03 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- @@ -373,47 +412,47 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.08 9.10 -| Nonbond 0.68 76.02 -| Bond 0.00 0.06 -| Angle 0.00 0.28 -| Dihedral 0.01 0.62 -| Shake 0.01 0.73 -| RunMD 0.11 12.86 -| Other 0.00 0.34 +| DataDistrib 0.01 1.88 +| Nonbond 0.40 83.91 +| Bond 0.00 0.10 +| Angle 0.00 0.10 +| Dihedral 0.00 0.31 +| Shake 0.00 0.52 +| RunMD 0.06 12.96 +| Other 0.00 0.21 | ------------------------------ -| Total 0.89 +| Total 0.48 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.06 -| Build List 0.04 4.60 +| Set Up Cit 0.00 0.42 +| Build List 0.05 9.72 | --------------------------------- -| Total 0.04 4.66 +| Total 0.05 10.14 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.43 48.18 -| Exclude Masked 0.01 0.84 -| Other 0.01 1.40 +| NonBonded Calc 0.23 47.86 +| Exclude Masked 0.00 0.73 +| Other 0.01 1.15 | --------------------------------- -| Total 0.45 50.42 +| Total 0.24 49.74 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.02 1.74 -| Grid Charges 0.02 2.08 -| Scalar Sum 0.02 2.75 -| Gradient Sum 0.02 2.53 -| FFT 0.10 11.79 +| 1D bspline 0.01 2.61 +| Grid Charges 0.01 2.30 +| Scalar Sum 0.02 3.87 +| Gradient Sum 0.01 2.72 +| FFT 0.06 12.54 | --------------------------------- -| Total 0.19 20.89 +| Total 0.11 24.03 | PME Load Balancing CPU Time, Average for All Tasks: | @@ -428,18 +467,18 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.80 Per Step(ms) = 17.81 -| ns/day = 9.70 seconds/ns = 8904.90 +| Elapsed(s) = 0.42 Per Step(ms) = 9.41 +| ns/day = 18.36 seconds/ns = 4705.88 | | Average timings for all steps: -| Elapsed(s) = 0.89 Per Step(ms) = 17.88 -| ns/day = 9.67 seconds/ns = 8939.00 +| Elapsed(s) = 0.48 Per Step(ms) = 9.58 +| ns/day = 18.04 seconds/ns = 4789.60 | ----------------------------------------------------- -| Master Setup CPU time: 0.08 seconds -| Master NonSetup CPU time: 0.89 seconds -| Master Total CPU time: 0.97 seconds 0.00 hours +| Master Setup CPU time: 0.05 seconds +| Master NonSetup CPU time: 0.48 seconds +| Master Total CPU time: 0.53 seconds 0.00 hours | Master Setup wall time: 0 seconds -| Master NonSetup wall time: 1 seconds -| Master Total wall time: 1 seconds 0.00 hours +| Master NonSetup wall time: 0 seconds +| Master Total wall time: 0 seconds 0.00 hours diff --git test/nfe/mwabmd/save.pmemd/mdout.3 test/nfe/mwabmd/save.pmemd/mdout.3 index 8858479509..7d8706005e 100644 --- test/nfe/mwabmd/save.pmemd/mdout.3 +++ test/nfe/mwabmd/save.pmemd/mdout.3 @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 06/06/2016 at 14:46:13 +| Run on 09/06/2018 at 20:58:38 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/mwabmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/mwabmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -37,7 +37,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -48,7 +48,7 @@ File Assignments: umbrella_file = 'umbrella.3.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.3.nc' @@ -62,6 +62,7 @@ File Assignments: / +| irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: @@ -177,7 +178,7 @@ NGLY | Dynamic Memory, Types Used: | Reals 245730 -| Integers 202051 +| Integers 211563 | Nonbonded Pairs Initial Allocation: 358302 @@ -236,133 +237,171 @@ NGLY NFE : selection algorithm parameters: NFE : NFE : selection_freq = 10 (0.0200 ps) - NFE : selection scoring constant = 0.010000 + NFE : selection scoring constant = 0.020000 NFE : selection criterion epsilon = 0.000000 NFE : NFE : () () () () () () () () () () () () () () () () () () () () () () () () NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 298.58 PRESS = 0.0 - Etot = -8245.0626 EKtot = 1888.2779 EPtot = -10133.3405 + Etot = -8245.0546 EKtot = 1888.2779 EPtot = -10133.3326 BOND = 35.8447 ANGLE = 58.9315 DIHED = 71.9497 1-4 NB = 30.1714 1-4 EEL = 529.0876 VDWAALS = 1322.0722 - EELEC = -12181.3976 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12181.3976 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10133.3405 Ewald error estimate: 0.3303E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.08 PRESS = 0.0 - Etot = -8235.4665 EKtot = 1916.7738 EPtot = -10152.2403 + Etot = -8235.4486 EKtot = 1916.7738 EPtot = -10152.2224 BOND = 29.8765 ANGLE = 64.3672 DIHED = 72.3614 1-4 NB = 29.6021 1-4 EEL = 524.6812 VDWAALS = 1325.8059 - EELEC = -12198.9346 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12198.9346 EHBOND = 0.0000 RESTRAINT = 0.0179 + EAMBER (non-restraint) = -10152.2403 Ewald error estimate: 0.4081E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NFE : Selection resampling : new 3 comes from 4 - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 278.59 PRESS = 0.0 - Etot = -8693.0840 EKtot = 1761.8518 EPtot = -10454.9358 - BOND = 33.0533 ANGLE = 63.5968 DIHED = 72.4230 - 1-4 NB = 29.9407 1-4 EEL = 527.2980 VDWAALS = 1313.0735 - EELEC = -12494.3211 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2015E-03 + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 + Etot = -8320.0172 EKtot = 1879.6571 EPtot = -10199.6743 + BOND = 25.7314 ANGLE = 67.7047 DIHED = 76.2864 + 1-4 NB = 31.4941 1-4 EEL = 535.0442 VDWAALS = 1359.5172 + EELEC = -12295.5101 EHBOND = 0.0000 RESTRAINT = 0.0576 + EAMBER (non-restraint) = -10199.7320 + Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 286.19 PRESS = 0.0 - Etot = -8675.6028 EKtot = 1809.9627 EPtot = -10485.5655 - BOND = 32.9786 ANGLE = 54.9065 DIHED = 76.9223 - 1-4 NB = 31.4771 1-4 EEL = 527.5529 VDWAALS = 1319.6219 - EELEC = -12529.0250 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1675E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.058 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 + Etot = -8311.8651 EKtot = 1892.0360 EPtot = -10203.9010 + BOND = 32.8322 ANGLE = 68.2453 DIHED = 72.8983 + 1-4 NB = 28.3884 1-4 EEL = 536.4092 VDWAALS = 1387.0687 + EELEC = -12329.8338 EHBOND = 0.0000 RESTRAINT = 0.0905 + EAMBER (non-restraint) = -10203.9916 + Ewald error estimate: 0.2635E-04 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 3 comes from 4 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.091 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 3 comes from 1 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 207.58 PRESS = 0.0 - Etot = -9052.2443 EKtot = 1312.7589 EPtot = -10365.0031 - BOND = 35.7629 ANGLE = 68.5522 DIHED = 74.1854 - 1-4 NB = 29.4268 1-4 EEL = 523.0756 VDWAALS = 1509.4788 - EELEC = -12605.4847 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.6609E-05 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 304.33 PRESS = 0.0 + Etot = -8214.7597 EKtot = 1924.6797 EPtot = -10139.4394 + BOND = 32.7375 ANGLE = 59.8108 DIHED = 81.8667 + 1-4 NB = 34.3189 1-4 EEL = 540.6806 VDWAALS = 1427.0107 + EELEC = -12315.9698 EHBOND = 0.0000 RESTRAINT = 0.1053 + EAMBER (non-restraint) = -10139.5446 + Ewald error estimate: 0.2810E-04 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 204.60 PRESS = 0.0 - Etot = -9037.1797 EKtot = 1293.9565 EPtot = -10331.1361 - BOND = 23.1663 ANGLE = 66.7049 DIHED = 74.4292 - 1-4 NB = 29.7417 1-4 EEL = 522.6784 VDWAALS = 1537.0056 - EELEC = -12584.8622 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1150E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.105 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 306.17 PRESS = 0.0 + Etot = -8217.6738 EKtot = 1936.3007 EPtot = -10153.9745 + BOND = 27.7620 ANGLE = 67.5250 DIHED = 80.3633 + 1-4 NB = 34.0498 1-4 EEL = 542.3720 VDWAALS = 1444.0653 + EELEC = -12350.2447 EHBOND = 0.0000 RESTRAINT = 0.1328 + EAMBER (non-restraint) = -10154.1073 + Ewald error estimate: 0.1700E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 3 comes from 4 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.133 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 3 comes from 2 - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 198.92 PRESS = 0.0 - Etot = -8915.0089 EKtot = 1257.9953 EPtot = -10173.0043 - BOND = 28.4603 ANGLE = 72.9866 DIHED = 71.6008 - 1-4 NB = 29.2044 1-4 EEL = 522.9230 VDWAALS = 1763.9939 - EELEC = -12662.1732 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1940E-03 + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 298.82 PRESS = 0.0 + Etot = -8216.1590 EKtot = 1889.7927 EPtot = -10105.9517 + BOND = 29.0913 ANGLE = 68.4372 DIHED = 79.1987 + 1-4 NB = 32.9257 1-4 EEL = 547.9543 VDWAALS = 1460.4301 + EELEC = -12324.1567 EHBOND = 0.0000 RESTRAINT = 0.1677 + EAMBER (non-restraint) = -10106.1194 + Ewald error estimate: 0.3806E-03 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 189.76 PRESS = 0.0 - Etot = -8902.0873 EKtot = 1200.0608 EPtot = -10102.1481 - BOND = 22.5075 ANGLE = 69.4212 DIHED = 76.5807 - 1-4 NB = 31.8838 1-4 EEL = 527.1246 VDWAALS = 1748.3096 - EELEC = -12577.9757 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2766E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.168 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 303.32 PRESS = 0.0 + Etot = -8210.6219 EKtot = 1918.2364 EPtot = -10128.8584 + BOND = 33.3262 ANGLE = 62.2842 DIHED = 76.5199 + 1-4 NB = 34.6190 1-4 EEL = 544.8030 VDWAALS = 1451.2291 + EELEC = -12331.8415 EHBOND = 0.0000 RESTRAINT = 0.2018 + EAMBER (non-restraint) = -10129.0601 + Ewald error estimate: 0.2168E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 3 comes from 4 - - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 189.34 PRESS = 0.0 - Etot = -8730.3592 EKtot = 1197.4479 EPtot = -9927.8071 - BOND = 27.6659 ANGLE = 77.4652 DIHED = 77.7717 - 1-4 NB = 29.6576 1-4 EEL = 532.3546 VDWAALS = 1960.9056 - EELEC = -12633.6277 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1695E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.202 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 308.05 PRESS = 0.0 + Etot = -8209.3146 EKtot = 1948.2060 EPtot = -10157.5205 + BOND = 33.8149 ANGLE = 59.8723 DIHED = 71.2879 + 1-4 NB = 35.6074 1-4 EEL = 545.7737 VDWAALS = 1439.7417 + EELEC = -12343.8574 EHBOND = 0.0000 RESTRAINT = 0.2391 + EAMBER (non-restraint) = -10157.7596 + Ewald error estimate: 0.1104E-04 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 195.79 PRESS = 0.0 - Etot = -8711.6632 EKtot = 1238.2323 EPtot = -9949.8955 - BOND = 28.1924 ANGLE = 62.4683 DIHED = 73.7736 - 1-4 NB = 29.6311 1-4 EEL = 526.1052 VDWAALS = 1882.8123 - EELEC = -12552.8785 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1452E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.239 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 297.05 PRESS = 0.0 + Etot = -8211.8490 EKtot = 1878.6031 EPtot = -10090.4521 + BOND = 31.0312 ANGLE = 65.2697 DIHED = 73.9875 + 1-4 NB = 31.4588 1-4 EEL = 541.2030 VDWAALS = 1452.8271 + EELEC = -12286.5031 EHBOND = 0.0000 RESTRAINT = 0.2737 + EAMBER (non-restraint) = -10090.7258 + Ewald error estimate: 0.2367E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 3 comes from 4 - + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.274 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 235.24 PRESS = 0.0 - Etot = -8719.7758 EKtot = 1487.7318 EPtot = -10207.5076 - BOND = 29.7508 ANGLE = 65.9400 DIHED = 74.1998 - 1-4 NB = 30.0737 1-4 EEL = 526.2881 VDWAALS = 1568.3079 - EELEC = -12502.0680 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2014E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.58 PRESS = 0.0 + Etot = -8239.2763 EKtot = 1907.2563 EPtot = -10146.5327 + BOND = 31.2048 ANGLE = 64.2448 DIHED = 75.6720 + 1-4 NB = 32.2636 1-4 EEL = 538.8009 VDWAALS = 1406.9768 + EELEC = -12295.8249 EHBOND = 0.0000 RESTRAINT = 0.1294 + EAMBER (non-restraint) = -10146.6621 + Ewald error estimate: 0.1951E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 46.74 PRESS = 0.0 - Etot = 273.0171 EKtot = 295.5844 EPtot = 185.4908 - BOND = 4.4596 ANGLE = 6.2681 DIHED = 2.1078 - 1-4 NB = 0.8455 1-4 EEL = 2.9197 VDWAALS = 239.7100 - EELEC = 162.5857 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1076E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.71 PRESS = 0.0 + Etot = 39.8866 EKtot = 23.4834 EPtot = 34.1357 + BOND = 2.9311 ANGLE = 3.5809 DIHED = 3.5845 + 1-4 NB = 2.2869 1-4 EEL = 7.0995 VDWAALS = 51.2001 + EELEC = 56.1242 EHBOND = 0.0000 RESTRAINT = 0.0860 + EAMBER (non-restraint) = 34.0496 + Ewald error estimate: 0.1393E-03 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- @@ -373,47 +412,47 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.07 8.03 -| Nonbond 0.69 77.87 -| Bond 0.00 0.06 -| Angle 0.00 0.17 -| Dihedral 0.01 0.67 -| Shake 0.01 0.96 -| RunMD 0.10 11.52 -| Other 0.01 0.73 +| DataDistrib 0.00 0.94 +| Nonbond 0.40 84.10 +| Bond 0.00 0.00 +| Angle 0.00 0.00 +| Dihedral 0.00 0.63 +| Shake 0.00 0.73 +| RunMD 0.06 13.39 +| Other 0.00 0.21 | ------------------------------ -| Total 0.89 +| Total 0.48 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.00 -| Build List 0.06 6.24 +| Set Up Cit 0.00 0.31 +| Build List 0.05 9.73 | --------------------------------- -| Total 0.06 6.24 +| Total 0.05 10.04 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.43 48.15 -| Exclude Masked 0.01 0.79 -| Other 0.01 0.90 +| NonBonded Calc 0.23 47.39 +| Exclude Masked 0.00 0.63 +| Other 0.01 1.67 | --------------------------------- -| Total 0.44 49.83 +| Total 0.24 49.69 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.02 1.74 -| Grid Charges 0.02 2.42 -| Scalar Sum 0.02 2.30 -| Gradient Sum 0.03 3.03 -| FFT 0.11 12.30 +| 1D bspline 0.01 2.51 +| Grid Charges 0.01 2.09 +| Scalar Sum 0.02 3.87 +| Gradient Sum 0.02 3.24 +| FFT 0.06 12.66 | --------------------------------- -| Total 0.19 21.80 +| Total 0.12 24.37 | PME Load Balancing CPU Time, Average for All Tasks: | @@ -428,18 +467,18 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.80 Per Step(ms) = 17.81 -| ns/day = 9.70 seconds/ns = 8905.80 +| Elapsed(s) = 0.42 Per Step(ms) = 9.41 +| ns/day = 18.36 seconds/ns = 4705.98 | | Average timings for all steps: -| Elapsed(s) = 0.90 Per Step(ms) = 17.96 -| ns/day = 9.62 seconds/ns = 8980.30 +| Elapsed(s) = 0.48 Per Step(ms) = 9.58 +| ns/day = 18.04 seconds/ns = 4789.33 | ----------------------------------------------------- -| Master Setup CPU time: 0.08 seconds -| Master NonSetup CPU time: 0.90 seconds -| Master Total CPU time: 0.98 seconds 0.00 hours +| Master Setup CPU time: 0.05 seconds +| Master NonSetup CPU time: 0.48 seconds +| Master Total CPU time: 0.53 seconds 0.00 hours | Master Setup wall time: 0 seconds -| Master NonSetup wall time: 1 seconds -| Master Total wall time: 1 seconds 0.00 hours +| Master NonSetup wall time: 0 seconds +| Master Total wall time: 0 seconds 0.00 hours diff --git test/nfe/mwabmd/save.pmemd/mdout.4 test/nfe/mwabmd/save.pmemd/mdout.4 index 8b66fa986e..0a1abfff9e 100644 --- test/nfe/mwabmd/save.pmemd/mdout.4 +++ test/nfe/mwabmd/save.pmemd/mdout.4 @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 06/06/2016 at 14:46:13 +| Run on 09/06/2018 at 20:58:38 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/mwabmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/mwabmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -37,7 +37,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &abmd @@ -48,7 +48,7 @@ File Assignments: umbrella_file = 'umbrella.4.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.4.nc' @@ -62,6 +62,7 @@ File Assignments: / +| irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: @@ -177,7 +178,7 @@ NGLY | Dynamic Memory, Types Used: | Reals 245734 -| Integers 202929 +| Integers 212441 | Nonbonded Pairs Initial Allocation: 358302 @@ -236,123 +237,169 @@ NGLY NFE : selection algorithm parameters: NFE : NFE : selection_freq = 10 (0.0200 ps) - NFE : selection scoring constant = 0.010000 + NFE : selection scoring constant = 0.020000 NFE : selection criterion epsilon = 0.000000 NFE : NFE : () () () () () () () () () () () () () () () () () () () () () () () () NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.4833 EKtot = 1914.1824 EPtot = -10235.6657 + Etot = -8321.4710 EKtot = 1914.1824 EPtot = -10235.6534 BOND = 19.0734 ANGLE = 63.5926 DIHED = 72.6962 1-4 NB = 31.9325 1-4 EEL = 541.0002 VDWAALS = 1297.2732 - EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0123 + EAMBER (non-restraint) = -10235.6657 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.012 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.15 PRESS = 0.0 - Etot = -8329.3298 EKtot = 1917.1639 EPtot = -10246.4937 + Etot = -8329.3030 EKtot = 1917.1639 EPtot = -10246.4669 BOND = 25.2751 ANGLE = 68.1066 DIHED = 73.1043 1-4 NB = 34.0178 1-4 EEL = 541.6435 VDWAALS = 1326.2609 - EELEC = -12314.9019 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9019 EHBOND = 0.0000 RESTRAINT = 0.0268 + EAMBER (non-restraint) = -10246.4937 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 243.22 PRESS = 0.0 - Etot = -8448.7987 EKtot = 1538.1576 EPtot = -9986.9563 - BOND = 25.2542 ANGLE = 73.3411 DIHED = 78.5680 - 1-4 NB = 31.2996 1-4 EEL = 537.5754 VDWAALS = 1453.2153 - EELEC = -12186.2099 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1661E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.027 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 + Etot = -8320.0172 EKtot = 1879.6571 EPtot = -10199.6743 + BOND = 25.7314 ANGLE = 67.7047 DIHED = 76.2864 + 1-4 NB = 31.4941 1-4 EEL = 535.0442 VDWAALS = 1359.5172 + EELEC = -12295.5101 EHBOND = 0.0000 RESTRAINT = 0.0576 + EAMBER (non-restraint) = -10199.7320 + Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 268.61 PRESS = 0.0 - Etot = -8437.9039 EKtot = 1698.7256 EPtot = -10136.6295 - BOND = 33.9540 ANGLE = 68.9694 DIHED = 72.4602 - 1-4 NB = 27.6053 1-4 EEL = 536.8942 VDWAALS = 1498.3740 - EELEC = -12374.8866 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8665E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.058 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 + Etot = -8311.8651 EKtot = 1892.0360 EPtot = -10203.9010 + BOND = 32.8322 ANGLE = 68.2453 DIHED = 72.8983 + 1-4 NB = 28.3884 1-4 EEL = 536.4092 VDWAALS = 1387.0687 + EELEC = -12329.8338 EHBOND = 0.0000 RESTRAINT = 0.0905 + EAMBER (non-restraint) = -10203.9916 + Ewald error estimate: 0.2635E-04 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 231.54 PRESS = 0.0 - Etot = -8421.9575 EKtot = 1464.3029 EPtot = -9886.2604 - BOND = 35.8135 ANGLE = 83.2837 DIHED = 75.0730 - 1-4 NB = 28.4348 1-4 EEL = 539.5576 VDWAALS = 1652.7750 - EELEC = -12301.1981 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1484E-03 - ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.091 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 4 comes from 2 - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 253.65 PRESS = 0.0 - Etot = -8405.9916 EKtot = 1604.1347 EPtot = -10010.1263 - BOND = 33.8795 ANGLE = 67.5739 DIHED = 75.3144 - 1-4 NB = 28.9503 1-4 EEL = 535.8513 VDWAALS = 1653.8466 - EELEC = -12405.5424 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1178E-04 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.81 PRESS = 0.0 + Etot = -8313.4691 EKtot = 1908.6890 EPtot = -10222.1581 + BOND = 35.4495 ANGLE = 70.8442 DIHED = 73.4768 + 1-4 NB = 28.8860 1-4 EEL = 538.8792 VDWAALS = 1406.8403 + EELEC = -12376.6460 EHBOND = 0.0000 RESTRAINT = 0.1119 + EAMBER (non-restraint) = -10222.2700 + Ewald error estimate: 0.3060E-04 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 227.42 PRESS = 0.0 - Etot = -8318.5407 EKtot = 1438.2278 EPtot = -9756.7685 - BOND = 25.3352 ANGLE = 82.3165 DIHED = 75.9510 - 1-4 NB = 29.7333 1-4 EEL = 533.8586 VDWAALS = 1788.6443 - EELEC = -12292.6074 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1028E-05 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.112 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.89 PRESS = 0.0 + Etot = -8308.0017 EKtot = 1947.1702 EPtot = -10255.1719 + BOND = 32.8681 ANGLE = 64.4530 DIHED = 74.4285 + 1-4 NB = 30.2000 1-4 EEL = 534.5115 VDWAALS = 1408.1052 + EELEC = -12399.8637 EHBOND = 0.0000 RESTRAINT = 0.1254 + EAMBER (non-restraint) = -10255.2973 + Ewald error estimate: 0.7443E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.125 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 4 comes from 3 - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 252.99 PRESS = 0.0 - Etot = -8306.8744 EKtot = 1599.9820 EPtot = -9906.8564 - BOND = 29.0167 ANGLE = 69.6871 DIHED = 73.5125 - 1-4 NB = 34.8784 1-4 EEL = 533.6851 VDWAALS = 1762.8572 - EELEC = -12410.4934 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1166E-04 - ------------------------------------------------------------------------------ + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 298.82 PRESS = 0.0 + Etot = -8216.1590 EKtot = 1889.7927 EPtot = -10105.9517 + BOND = 29.0913 ANGLE = 68.4372 DIHED = 79.1987 + 1-4 NB = 32.9257 1-4 EEL = 547.9543 VDWAALS = 1460.4301 + EELEC = -12324.1567 EHBOND = 0.0000 RESTRAINT = 0.1677 + EAMBER (non-restraint) = -10106.1194 + Ewald error estimate: 0.3806E-03 + ------------------------------------------------------------------------------ - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 224.11 PRESS = 0.0 - Etot = -8245.1803 EKtot = 1417.3163 EPtot = -9662.4966 - BOND = 29.9011 ANGLE = 84.9392 DIHED = 76.2004 - 1-4 NB = 36.1182 1-4 EEL = 535.1800 VDWAALS = 1903.3823 - EELEC = -12328.2178 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8805E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.168 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 303.32 PRESS = 0.0 + Etot = -8210.6219 EKtot = 1918.2364 EPtot = -10128.8584 + BOND = 33.3262 ANGLE = 62.2842 DIHED = 76.5199 + 1-4 NB = 34.6190 1-4 EEL = 544.8030 VDWAALS = 1451.2291 + EELEC = -12331.8415 EHBOND = 0.0000 RESTRAINT = 0.2018 + EAMBER (non-restraint) = -10129.0601 + Ewald error estimate: 0.2168E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.202 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 308.05 PRESS = 0.0 + Etot = -8209.3146 EKtot = 1948.2060 EPtot = -10157.5205 + BOND = 33.8149 ANGLE = 59.8723 DIHED = 71.2879 + 1-4 NB = 35.6074 1-4 EEL = 545.7737 VDWAALS = 1439.7417 + EELEC = -12343.8574 EHBOND = 0.0000 RESTRAINT = 0.2391 + EAMBER (non-restraint) = -10157.7596 + Ewald error estimate: 0.1104E-04 + ------------------------------------------------------------------------------ - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 250.22 PRESS = 0.0 - Etot = -8239.6999 EKtot = 1582.4488 EPtot = -9822.1486 - BOND = 24.1972 ANGLE = 72.6575 DIHED = 72.3694 - 1-4 NB = 34.8706 1-4 EEL = 539.2487 VDWAALS = 1876.6554 - EELEC = -12442.1474 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1306E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.239 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 297.05 PRESS = 0.0 + Etot = -8211.8490 EKtot = 1878.6031 EPtot = -10090.4521 + BOND = 31.0312 ANGLE = 65.2697 DIHED = 73.9875 + 1-4 NB = 31.4588 1-4 EEL = 541.2030 VDWAALS = 1452.8271 + EELEC = -12286.5031 EHBOND = 0.0000 RESTRAINT = 0.2737 + EAMBER (non-restraint) = -10090.7258 + Ewald error estimate: 0.2367E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.274 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 255.76 PRESS = 0.0 - Etot = -8347.5760 EKtot = 1617.4642 EPtot = -9965.0402 - BOND = 28.1700 ANGLE = 73.4468 DIHED = 74.5249 - 1-4 NB = 31.7841 1-4 EEL = 537.4495 VDWAALS = 1621.3284 - EELEC = -12331.7439 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1500E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.91 PRESS = 0.0 + Etot = -8275.2072 EKtot = 1909.3737 EPtot = -10184.5808 + BOND = 29.8493 ANGLE = 65.8810 DIHED = 74.3885 + 1-4 NB = 31.9530 1-4 EEL = 540.7222 VDWAALS = 1398.9294 + EELEC = -12326.4348 EHBOND = 0.0000 RESTRAINT = 0.1307 + EAMBER (non-restraint) = -10184.7115 + Ewald error estimate: 0.1975E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 26.84 PRESS = 0.0 - Etot = 72.7913 EKtot = 169.7372 EPtot = 186.9036 - BOND = 5.0164 ANGLE = 7.0883 DIHED = 1.9341 - 1-4 NB = 2.8991 1-4 EEL = 2.7013 VDWAALS = 207.4305 - EELEC = 73.8989 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1613E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.75 PRESS = 0.0 + Etot = 51.9345 EKtot = 23.6923 EPtot = 56.8459 + BOND = 4.8287 ANGLE = 3.1895 DIHED = 2.2051 + 1-4 NB = 2.2652 1-4 EEL = 4.3410 VDWAALS = 53.4263 + EELEC = 38.9840 EHBOND = 0.0000 RESTRAINT = 0.0841 + EAMBER (non-restraint) = 56.7617 + Ewald error estimate: 0.1699E-03 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- @@ -363,47 +410,47 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.06 7.07 -| Nonbond 0.71 80.09 +| DataDistrib 0.01 2.30 +| Nonbond 0.40 83.79 | Bond 0.00 0.00 -| Angle 0.00 0.06 -| Dihedral 0.01 0.73 -| Shake 0.01 0.73 -| RunMD 0.09 10.66 -| Other 0.01 0.67 +| Angle 0.00 0.10 +| Dihedral 0.00 0.84 +| Shake 0.00 0.52 +| RunMD 0.06 12.13 +| Other 0.00 0.31 | ------------------------------ -| Total 0.89 +| Total 0.48 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.06 -| Build List 0.07 7.85 +| Set Up Cit 0.00 0.21 +| Build List 0.05 9.73 | --------------------------------- -| Total 0.07 7.91 +| Total 0.05 9.94 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.43 48.29 -| Exclude Masked 0.01 1.12 -| Other 0.01 1.18 +| NonBonded Calc 0.23 47.49 +| Exclude Masked 0.01 1.15 +| Other 0.00 0.84 | --------------------------------- -| Total 0.45 50.59 +| Total 0.24 49.48 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.01 1.63 -| Grid Charges 0.02 2.36 -| Scalar Sum 0.02 2.36 -| Gradient Sum 0.02 2.13 -| FFT 0.12 13.12 +| 1D bspline 0.01 2.61 +| Grid Charges 0.01 2.20 +| Scalar Sum 0.02 3.24 +| Gradient Sum 0.01 2.82 +| FFT 0.06 13.49 | --------------------------------- -| Total 0.19 21.59 +| Total 0.12 24.37 | PME Load Balancing CPU Time, Average for All Tasks: | @@ -418,18 +465,18 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.80 Per Step(ms) = 17.81 -| ns/day = 9.70 seconds/ns = 8905.81 +| Elapsed(s) = 0.42 Per Step(ms) = 9.41 +| ns/day = 18.36 seconds/ns = 4705.89 | | Average timings for all steps: -| Elapsed(s) = 0.90 Per Step(ms) = 17.95 -| ns/day = 9.63 seconds/ns = 8973.66 +| Elapsed(s) = 0.48 Per Step(ms) = 9.58 +| ns/day = 18.04 seconds/ns = 4788.58 | ----------------------------------------------------- -| Master Setup CPU time: 0.08 seconds -| Master NonSetup CPU time: 0.89 seconds -| Master Total CPU time: 0.97 seconds 0.00 hours +| Master Setup CPU time: 0.05 seconds +| Master NonSetup CPU time: 0.48 seconds +| Master Total CPU time: 0.53 seconds 0.00 hours | Master Setup wall time: 0 seconds -| Master NonSetup wall time: 1 seconds -| Master Total wall time: 1 seconds 0.00 hours +| Master NonSetup wall time: 0 seconds +| Master Total wall time: 0 seconds 0.00 hours diff --git test/nfe/mwabmd/save.pmemd/umbrella.1.ncdump test/nfe/mwabmd/save.pmemd/umbrella.1.ncdump new file mode 100644 index 0000000000..50725ca804 --- /dev/null +++ test/nfe/mwabmd/save.pmemd/umbrella.1.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0502425533, 0.2579158286, 0.3393774594, + 0.1844807562, 0.0618658170, 0.0003049922, 0.0000000000, + 0.0000000000, 0.0008648204, 0.0164693435, 0.0229234400, + 0.0096243675, 0.0000000000, 0.0043973768, 0.0205066390, + 0.0206277057, 0.0045667847, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.pmemd/umbrella.2.ncdump test/nfe/mwabmd/save.pmemd/umbrella.2.ncdump new file mode 100644 index 0000000000..50725ca804 --- /dev/null +++ test/nfe/mwabmd/save.pmemd/umbrella.2.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0502425533, 0.2579158286, 0.3393774594, + 0.1844807562, 0.0618658170, 0.0003049922, 0.0000000000, + 0.0000000000, 0.0008648204, 0.0164693435, 0.0229234400, + 0.0096243675, 0.0000000000, 0.0043973768, 0.0205066390, + 0.0206277057, 0.0045667847, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.pmemd/umbrella.3.ncdump test/nfe/mwabmd/save.pmemd/umbrella.3.ncdump new file mode 100644 index 0000000000..50725ca804 --- /dev/null +++ test/nfe/mwabmd/save.pmemd/umbrella.3.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0502425533, 0.2579158286, 0.3393774594, + 0.1844807562, 0.0618658170, 0.0003049922, 0.0000000000, + 0.0000000000, 0.0008648204, 0.0164693435, 0.0229234400, + 0.0096243675, 0.0000000000, 0.0043973768, 0.0205066390, + 0.0206277057, 0.0045667847, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.pmemd/umbrella.4.ncdump test/nfe/mwabmd/save.pmemd/umbrella.4.ncdump new file mode 100644 index 0000000000..50725ca804 --- /dev/null +++ test/nfe/mwabmd/save.pmemd/umbrella.4.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0502425533, 0.2579158286, 0.3393774594, + 0.1844807562, 0.0618658170, 0.0003049922, 0.0000000000, + 0.0000000000, 0.0008648204, 0.0164693435, 0.0229234400, + 0.0096243675, 0.0000000000, 0.0043973768, 0.0205066390, + 0.0206277057, 0.0045667847, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.pmemd/wt_umbrella.1.ncdump test/nfe/mwabmd/save.pmemd/wt_umbrella.1.ncdump new file mode 100644 index 0000000000..2d5e490eee --- /dev/null +++ test/nfe/mwabmd/save.pmemd/wt_umbrella.1.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0517498299, 0.2656533035, 0.3495587832, + 0.1900151789, 0.0637217915, 0.0003141419, 0.0000000000, + 0.0000000000, 0.0008907650, 0.0169634238, 0.0236111432, + 0.0099130985, 0.0000000000, 0.0045292981, 0.0211218382, + 0.0212465369, 0.0047037883, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.pmemd/wt_umbrella.2.ncdump test/nfe/mwabmd/save.pmemd/wt_umbrella.2.ncdump new file mode 100644 index 0000000000..2d5e490eee --- /dev/null +++ test/nfe/mwabmd/save.pmemd/wt_umbrella.2.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0517498299, 0.2656533035, 0.3495587832, + 0.1900151789, 0.0637217915, 0.0003141419, 0.0000000000, + 0.0000000000, 0.0008907650, 0.0169634238, 0.0236111432, + 0.0099130985, 0.0000000000, 0.0045292981, 0.0211218382, + 0.0212465369, 0.0047037883, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.pmemd/wt_umbrella.3.ncdump test/nfe/mwabmd/save.pmemd/wt_umbrella.3.ncdump new file mode 100644 index 0000000000..2d5e490eee --- /dev/null +++ test/nfe/mwabmd/save.pmemd/wt_umbrella.3.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0517498299, 0.2656533035, 0.3495587832, + 0.1900151789, 0.0637217915, 0.0003141419, 0.0000000000, + 0.0000000000, 0.0008907650, 0.0169634238, 0.0236111432, + 0.0099130985, 0.0000000000, 0.0045292981, 0.0211218382, + 0.0212465369, 0.0047037883, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.pmemd/wt_umbrella.4.ncdump test/nfe/mwabmd/save.pmemd/wt_umbrella.4.ncdump new file mode 100644 index 0000000000..2d5e490eee --- /dev/null +++ test/nfe/mwabmd/save.pmemd/wt_umbrella.4.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0517498299, 0.2656533035, 0.3495587832, + 0.1900151789, 0.0637217915, 0.0003141419, 0.0000000000, + 0.0000000000, 0.0008907650, 0.0169634238, 0.0236111432, + 0.0099130985, 0.0000000000, 0.0045292981, 0.0211218382, + 0.0212465369, 0.0047037883, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.sander/abmd.1.txt test/nfe/mwabmd/save.sander/abmd.1.txt index 4623cbb63c..b19cdd2638 100644 --- test/nfe/mwabmd/save.sander/abmd.1.txt +++ test/nfe/mwabmd/save.sander/abmd.1.txt @@ -12,42 +12,42 @@ 0.0160 6.3420914451 0.0251678631 0.0180 6.3421608025 0.0282217244 0.0200 6.3417450466 0.0312104757 - 0.0220 6.3408983394 0.0351477783 - 0.0240 6.3395418603 0.0389693096 - 0.0260 6.3376745809 0.0426504033 - 0.0280 6.3357027550 0.0462384233 - 0.0300 6.3338172815 0.0497612679 - 0.0320 6.3322684964 0.0532716398 - 0.0340 6.3311790136 0.0568124354 - 0.0360 6.3308491363 0.0604852671 - 0.0380 6.3312081621 0.0643085000 - 0.0400 6.3320244568 0.0682514948 - 0.0420 6.3329859479 0.0742230012 - 0.0440 6.3336106834 0.0800801793 - 0.0460 6.3337681005 0.0857600394 - 0.0480 6.3333320069 0.0911862852 - 0.0500 6.3325619610 0.0964267895 - 0.0520 6.3316206888 0.1015238903 - 0.0540 6.3305119632 0.1064688010 - 0.0560 6.3296347655 0.1114357148 - 0.0580 6.3291589933 0.1165252149 - 0.0600 6.3291593297 0.1218044551 - 0.0620 6.3292643567 0.1271171512 - 0.0640 6.3293505873 0.1324155180 - 0.0660 6.3292585038 0.1376206356 - 0.0680 6.3287638810 0.1426051319 - 0.0700 6.3282434201 0.1475656569 - 0.0720 6.3280030265 0.1526786454 - 0.0740 6.3280346722 0.1579458782 - 0.0760 6.3284456986 0.1634371361 - 0.0780 6.3293464516 0.1692338129 - 0.0800 6.3306628126 0.1752982578 - 0.0820 6.3320750249 0.1827577801 - 0.0840 6.3336627986 0.1903239885 - 0.0860 6.3350593774 0.1977633739 - 0.0880 6.3360307393 0.2049297767 - 0.0900 6.3366711519 0.2118851699 - 0.0920 6.3371161356 0.2187170568 - 0.0940 6.3375764047 0.2255623297 - 0.0960 6.3382864395 0.2325733890 - 0.0980 6.3393770033 0.2398327863 + 0.0220 6.3409539706 0.0361702493 + 0.0240 6.3396818636 0.0409909930 + 0.0260 6.3380508045 0.0456644111 + 0.0280 6.3362885818 0.0502165750 + 0.0300 6.3346747123 0.0546996235 + 0.0320 6.3335283794 0.0592030804 + 0.0340 6.3329405383 0.0637832831 + 0.0360 6.3331347378 0.0685523276 + 0.0380 6.3337403439 0.0734267832 + 0.0400 6.3346081856 0.0783832714 + 0.0420 6.3353872052 0.0855223910 + 0.0440 6.3356516044 0.0924392672 + 0.0460 6.3352652762 0.0990620249 + 0.0480 6.3339976604 0.1052660024 + 0.0500 6.3320781773 0.1111203750 + 0.0520 6.3295860245 0.1166293106 + 0.0540 6.3270094918 0.1220050917 + 0.0560 6.3246049212 0.1273750396 + 0.0580 6.3224770635 0.1328065508 + 0.0600 6.3209593711 0.1384989099 + 0.0620 6.3198223028 0.1457875296 + 0.0640 6.3189435539 0.1532097134 + 0.0660 6.3179362096 0.1605529883 + 0.0680 6.3165101225 0.1676510045 + 0.0700 6.3146987063 0.1745126427 + 0.0720 6.3125703609 0.1811654309 + 0.0740 6.3105094188 0.1878282921 + 0.0760 6.3087251538 0.1946316199 + 0.0780 6.3074898352 0.2017540196 + 0.0800 6.3067147290 0.2091529746 + 0.0820 6.3061912408 0.2167040286 + 0.0840 6.3058928831 0.2243930744 + 0.0860 6.3053444400 0.2319191674 + 0.0880 6.3042509901 0.2390884518 + 0.0900 6.3027144700 0.2459529189 + 0.0920 6.3009358589 0.2526302765 + 0.0940 6.2992254260 0.2593236072 + 0.0960 6.2979413879 0.2662889452 + 0.0980 6.2973169135 0.2737077303 diff --git test/nfe/mwabmd/save.sander/abmd.2.txt test/nfe/mwabmd/save.sander/abmd.2.txt index 3675c15ecd..7eb92fb2db 100644 --- test/nfe/mwabmd/save.sander/abmd.2.txt +++ test/nfe/mwabmd/save.sander/abmd.2.txt @@ -1,28 +1,28 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0020 7.3436195531 0.0019947857 - 0.0060 7.3462553532 0.0059844210 - 0.0100 7.3506175249 0.0099703971 - 0.0140 7.3557487885 0.0139438102 - 0.0180 7.3594474244 0.0179111196 - 0.0220 7.9361269255 0.0218837864 - 0.0260 7.9356405214 0.0258597164 - 0.0300 7.9383011516 0.0298381777 - 0.0340 7.9441365592 0.0337780886 - 0.0380 7.9491754325 0.0376740682 - 0.0420 6.3328847958 0.0741899599 - 0.0460 6.3334646393 0.0856501008 - 0.0500 6.3318900501 0.0961564307 - 0.0540 6.3291246347 0.1058523779 - 0.0580 6.3269898174 0.1154775209 - 0.0620 6.3263297295 0.1256028681 - 0.0660 6.3260168110 0.1358428504 - 0.0700 6.3243887433 0.1453090151 - 0.0740 6.3221722783 0.1542990163 - 0.0780 6.3213254921 0.1640018764 - 0.0820 6.3221945377 0.1761712574 - 0.0860 6.3234782007 0.1900068042 - 0.0900 6.3230231290 0.2025963314 - 0.0940 6.3217459469 0.2145472779 - 0.0980 6.3219127903 0.2275599010 + 0.0000 7.3427665757 0.0000000000 + 0.0040 7.3446895772 0.0039896524 + 0.0080 7.3482807687 0.0079783806 + 0.0120 7.3532386361 0.0119588849 + 0.0160 7.3578770687 0.0159269124 + 0.0200 6.4915905107 0.0296790296 + 0.0240 6.4919906017 0.0436237525 + 0.0280 6.4914538535 0.0576241602 + 0.0320 6.4931911614 0.0712030111 + 0.0360 6.4974584933 0.0841759714 + 0.0400 6.3346081856 0.0783832714 + 0.0440 6.3356516044 0.0924392672 + 0.0480 6.3339976604 0.1052660024 + 0.0520 6.3295860245 0.1166293106 + 0.0560 6.3246049212 0.1273750396 + 0.0600 6.3209593711 0.1384989099 + 0.0640 6.3189435539 0.1532097134 + 0.0680 6.3165101225 0.1676510045 + 0.0720 6.3125703609 0.1811654309 + 0.0760 6.3087251538 0.1946316199 + 0.0800 6.3067147290 0.2091529746 + 0.0840 6.3058928831 0.2243930744 + 0.0880 6.3042509901 0.2390884518 + 0.0920 6.3009358589 0.2526302765 + 0.0960 6.2979413879 0.2662889452 diff --git test/nfe/mwabmd/save.sander/abmd.3.txt test/nfe/mwabmd/save.sander/abmd.3.txt index f3a91feaec..0d6213b9f8 100644 --- test/nfe/mwabmd/save.sander/abmd.3.txt +++ test/nfe/mwabmd/save.sander/abmd.3.txt @@ -1,19 +1,20 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0040 7.9395458755 0.0039809175 - 0.0100 7.9366475289 0.0099486200 - 0.0160 7.9367675931 0.0159177917 - 0.0220 6.4920440751 0.0346332458 - 0.0280 6.4915101274 0.0496316046 - 0.0340 6.4951403349 0.0637698029 - 0.0400 6.5016922820 0.0769545259 - 0.0460 6.5073501540 0.0922806601 - 0.0520 6.5144150503 0.1064069217 - 0.0580 6.5210861865 0.1196443692 - 0.0640 6.5224879203 0.1345930663 - 0.0700 6.5210708039 0.1508732669 - 0.0760 6.5229415122 0.1652751738 - 0.0820 6.3221945377 0.1761712574 - 0.0880 6.3234623935 0.1964571070 - 0.0940 6.3217459469 0.2145472779 + 0.0000 7.9425702652 0.0000000000 + 0.0060 7.9382950103 0.0059704516 + 0.0120 7.9364275347 0.0119380949 + 0.0180 7.9368124157 0.0179071215 + 0.0240 6.4919906017 0.0436237525 + 0.0300 6.4919880836 0.0644819739 + 0.0360 6.4974584933 0.0841759714 + 0.0420 6.3353872052 0.0855223910 + 0.0480 6.3339976604 0.1052660024 + 0.0540 6.3270094918 0.1220050917 + 0.0600 6.3209593711 0.1384989099 + 0.0660 6.3179362096 0.1605529883 + 0.0720 6.3125703609 0.1811654309 + 0.0780 6.3074898352 0.2017540196 + 0.0840 6.3058928831 0.2243930744 + 0.0900 6.3027144700 0.2459529189 + 0.0960 6.2979413879 0.2662889452 diff --git test/nfe/mwabmd/save.sander/abmd.4.txt test/nfe/mwabmd/save.sander/abmd.4.txt index 0e9eb8c1da..ab2b5b1cda 100644 --- test/nfe/mwabmd/save.sander/abmd.4.txt +++ test/nfe/mwabmd/save.sander/abmd.4.txt @@ -1,13 +1,13 @@ # # MD time (ps), CV #1, E_{bias} (kcal/mol) # - 0.0080 6.4782576403 0.0122506568 - 0.0180 6.4904463792 0.0267730498 - 0.0280 6.4915101274 0.0496316046 - 0.0380 6.4995984876 0.0725928162 - 0.0480 6.5094168618 0.0971924513 - 0.0580 6.5210861865 0.1196443692 - 0.0680 6.5213760885 0.1455283187 - 0.0780 6.5242828597 0.1695885160 - 0.0880 6.5292197871 0.1860111995 - 0.0980 6.5270710826 0.2059718182 + 0.0000 6.4718101196 0.0000000000 + 0.0100 6.4805813972 0.0152386065 + 0.0200 6.4915905107 0.0296790296 + 0.0300 6.4919880836 0.0644819739 + 0.0400 6.5020503277 0.0968500840 + 0.0500 6.5136784005 0.1150166701 + 0.0600 6.3209593711 0.1384989099 + 0.0700 6.3146987063 0.1745126427 + 0.0800 6.3067147290 0.2091529746 + 0.0900 6.3027144700 0.2459529189 diff --git test/nfe/mwabmd/save.sander/mdout.1 test/nfe/mwabmd/save.sander/mdout.1 index 54ee72ad7b..e36bdc9d49 100644 --- test/nfe/mwabmd/save.sander/mdout.1 +++ test/nfe/mwabmd/save.sander/mdout.1 @@ -3,11 +3,11 @@ Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 04/10/2018 at 14:01:49 +| Run on 09/04/2018 at 15:33:20 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/mwabmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/mwabmd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -57,7 +57,7 @@ File Assignments: umbrella_file = 'umbrella.1.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.1.nc' @@ -97,8 +97,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 113677 -| Total 7701 kbytes +| nblist Int 124375 +| Total 7742 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -169,13 +169,13 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 1571 3143 +| 0 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 2 nodes +| Running AMBER/MPI version on 1 nodes -| MULTISANDER: 4 groups. 2 processors out of 8 total. +| MULTISANDER: 4 groups. 1 processors out of 4 total. -------------------------------------------------------------------------------- 4. RESULTS @@ -211,7 +211,7 @@ NGLY NFE : selection algorithm parameters: NFE : NFE : selection_freq = 10 (0.0200 ps) - NFE : selection scoring constant = 0.010000 + NFE : selection scoring constant = 0.020000 NFE : selection criterion epsilon = 0.000000 NFE : NFE : () () () () () () () () () () () () () () () () () () () () () () () () @@ -227,152 +227,192 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 320505 +| Local SIZE OF NONBOND LIST = 650603 | TOTAL SIZE OF NONBOND LIST = 650603 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 310.12 PRESS = 0.0 - Etot = -8188.7886 EKtot = 1961.2513 EPtot = -10150.0400 + Etot = -8188.7760 EKtot = 1961.2513 EPtot = -10150.0274 BOND = 25.3727 ANGLE = 58.6639 DIHED = 80.8338 1-4 NB = 30.8521 1-4 EEL = 539.4401 VDWAALS = 1403.2404 - EELEC = -12288.4429 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12288.4429 EHBOND = 0.0000 RESTRAINT = 0.0126 + EAMBER (non-restraint) = -10150.0400 Ewald error estimate: 0.2391E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.013 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 311.17 PRESS = 0.0 - Etot = -8196.4686 EKtot = 1967.9098 EPtot = -10164.3783 + Etot = -8196.4403 EKtot = 1967.9098 EPtot = -10164.3501 BOND = 25.7998 ANGLE = 67.0917 DIHED = 76.2276 1-4 NB = 30.3557 1-4 EEL = 538.9007 VDWAALS = 1409.3611 - EELEC = -12312.1148 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12312.1148 EHBOND = 0.0000 RESTRAINT = 0.0282 + EAMBER (non-restraint) = -10164.3783 Ewald error estimate: 0.1858E-03 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.020147 / 0.072510 = 0.278 => 1 walker(s) - NFE : selection score for walker 2 is 0.003269 / 0.072510 = 0.045 => 0 walker(s) - NFE : selection score for walker 3 is 0.005663 / 0.072510 = 0.078 => 1 walker(s) - NFE : selection score for walker 4 is 0.043432 / 0.072510 = 0.599 => 2 walker(s) - NFE : Selection entropy 0.384606 is greater than threshold 0.000000 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.028 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.000406 / 0.002335 = 0.174 => 1 walker(s) + NFE : selection score for walker 2 is 0.000011 / 0.002335 = 0.005 => 0 walker(s) + NFE : selection score for walker 3 is 0.000032 / 0.002335 = 0.014 => 0 walker(s) + NFE : selection score for walker 4 is 0.001886 / 0.002335 = 0.808 => 3 walker(s) + NFE : Selection entropy 0.826228 is greater than threshold 0.000000 |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 250.78 PRESS = 0.0 - Etot = -8321.0982 EKtot = 1586.0107 EPtot = -9907.1089 - BOND = 35.0618 ANGLE = 57.2982 DIHED = 80.4934 - 1-4 NB = 30.7210 1-4 EEL = 543.2171 VDWAALS = 1528.7649 - EELEC = -12182.6653 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2817E-03 + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 309.48 PRESS = 0.0 + Etot = -8204.9670 EKtot = 1957.2209 EPtot = -10162.1879 + BOND = 34.4841 ANGLE = 56.5594 DIHED = 80.4516 + 1-4 NB = 30.5678 1-4 EEL = 543.5502 VDWAALS = 1421.4784 + EELEC = -12329.3296 EHBOND = 0.0000 RESTRAINT = 0.0502 + EAMBER (non-restraint) = -10162.2381 + Ewald error estimate: 0.2032E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 272.72 PRESS = 0.0 - Etot = -8322.0154 EKtot = 1724.7210 EPtot = -10046.7364 - BOND = 28.4343 ANGLE = 57.1236 DIHED = 79.4775 - 1-4 NB = 34.3363 1-4 EEL = 539.9308 VDWAALS = 1531.7877 - EELEC = -12317.8267 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1149E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.050 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 304.13 PRESS = 0.0 + Etot = -8219.7331 EKtot = 1923.3656 EPtot = -10143.0986 + BOND = 27.5327 ANGLE = 56.0018 DIHED = 79.6719 + 1-4 NB = 34.6043 1-4 EEL = 539.8766 VDWAALS = 1425.5446 + EELEC = -12306.4039 EHBOND = 0.0000 RESTRAINT = 0.0734 + EAMBER (non-restraint) = -10143.1720 + Ewald error estimate: 0.9427E-04 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.043537 / 0.100641 = 0.433 => 2 walker(s) - NFE : selection score for walker 2 is 0.005620 / 0.100641 = 0.056 => 0 walker(s) - NFE : selection score for walker 3 is 0.025742 / 0.100641 = 0.256 => 1 walker(s) - NFE : selection score for walker 4 is 0.025742 / 0.100641 = 0.256 => 1 walker(s) - NFE : Selection entropy 0.165200 is greater than threshold 0.000000 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.073 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.003264 / 0.004166 = 0.784 => 3 walker(s) + NFE : selection score for walker 2 is 0.000301 / 0.004166 = 0.072 => 1 walker(s) + NFE : selection score for walker 3 is 0.000301 / 0.004166 = 0.072 => 0 walker(s) + NFE : selection score for walker 4 is 0.000301 / 0.004166 = 0.072 => 0 walker(s) + NFE : Selection entropy 0.626047 is greater than threshold 0.000000 |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 243.30 PRESS = 0.0 - Etot = -8283.9039 EKtot = 1538.6860 EPtot = -9822.5900 - BOND = 30.6933 ANGLE = 65.5750 DIHED = 79.9655 - 1-4 NB = 33.8805 1-4 EEL = 539.8717 VDWAALS = 1638.7885 - EELEC = -12211.3645 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8069E-04 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 304.33 PRESS = 0.0 + Etot = -8214.7597 EKtot = 1924.6797 EPtot = -10139.4394 + BOND = 32.7375 ANGLE = 59.8108 DIHED = 81.8667 + 1-4 NB = 34.3189 1-4 EEL = 540.6806 VDWAALS = 1427.0107 + EELEC = -12315.9698 EHBOND = 0.0000 RESTRAINT = 0.1053 + EAMBER (non-restraint) = -10139.5446 + Ewald error estimate: 0.2810E-04 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 260.34 PRESS = 0.0 - Etot = -8276.9126 EKtot = 1646.4581 EPtot = -9923.3707 - BOND = 27.7116 ANGLE = 69.8071 DIHED = 78.2476 - 1-4 NB = 33.8576 1-4 EEL = 539.9648 VDWAALS = 1629.0331 - EELEC = -12301.9925 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8360E-05 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.105 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 306.17 PRESS = 0.0 + Etot = -8217.6738 EKtot = 1936.3007 EPtot = -10153.9745 + BOND = 27.7620 ANGLE = 67.5250 DIHED = 80.3633 + 1-4 NB = 34.0498 1-4 EEL = 542.3720 VDWAALS = 1444.0653 + EELEC = -12350.2447 EHBOND = 0.0000 RESTRAINT = 0.1328 + EAMBER (non-restraint) = -10154.1073 + Ewald error estimate: 0.1700E-03 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.059286 / 0.198407 = 0.299 => 1 walker(s) - NFE : selection score for walker 2 is 0.061605 / 0.198407 = 0.310 => 1 walker(s) - NFE : selection score for walker 3 is 0.038758 / 0.198407 = 0.195 => 1 walker(s) - NFE : selection score for walker 4 is 0.038758 / 0.198407 = 0.195 => 1 walker(s) - NFE : Selection entropy 0.024204 is greater than threshold 0.000000 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.133 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.003278 / 0.011899 = 0.275 => 2 walker(s) + NFE : selection score for walker 2 is 0.003278 / 0.011899 = 0.275 => 1 walker(s) + NFE : selection score for walker 3 is 0.003278 / 0.011899 = 0.275 => 1 walker(s) + NFE : selection score for walker 4 is 0.002066 / 0.011899 = 0.174 => 0 walker(s) + NFE : Selection entropy 0.016849 is greater than threshold 0.000000 |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 241.02 PRESS = 0.0 - Etot = -8187.0033 EKtot = 1524.2818 EPtot = -9711.2851 - BOND = 33.2631 ANGLE = 69.5949 DIHED = 77.9700 - 1-4 NB = 33.2640 1-4 EEL = 542.8941 VDWAALS = 1733.2338 - EELEC = -12201.5051 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2823E-03 + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 298.82 PRESS = 0.0 + Etot = -8216.1590 EKtot = 1889.7927 EPtot = -10105.9517 + BOND = 29.0913 ANGLE = 68.4372 DIHED = 79.1987 + 1-4 NB = 32.9257 1-4 EEL = 547.9543 VDWAALS = 1460.4301 + EELEC = -12324.1567 EHBOND = 0.0000 RESTRAINT = 0.1677 + EAMBER (non-restraint) = -10106.1194 + Ewald error estimate: 0.3806E-03 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 269.07 PRESS = 0.0 - Etot = -8183.1757 EKtot = 1701.6649 EPtot = -9884.8406 - BOND = 34.4238 ANGLE = 61.4770 DIHED = 75.1602 - 1-4 NB = 35.2175 1-4 EEL = 538.3448 VDWAALS = 1703.9328 - EELEC = -12333.3967 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3266E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.168 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 303.32 PRESS = 0.0 + Etot = -8210.6219 EKtot = 1918.2364 EPtot = -10128.8584 + BOND = 33.3262 ANGLE = 62.2842 DIHED = 76.5199 + 1-4 NB = 34.6190 1-4 EEL = 544.8030 VDWAALS = 1451.2291 + EELEC = -12331.8415 EHBOND = 0.0000 RESTRAINT = 0.2018 + EAMBER (non-restraint) = -10129.0601 + Ewald error estimate: 0.2168E-03 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.066854 / 0.272050 = 0.246 => 1 walker(s) - NFE : selection score for walker 2 is 0.077951 / 0.272050 = 0.287 => 2 walker(s) - NFE : selection score for walker 3 is 0.063622 / 0.272050 = 0.234 => 1 walker(s) - NFE : selection score for walker 4 is 0.063622 / 0.272050 = 0.234 => 0 walker(s) - NFE : Selection entropy 0.003649 is greater than threshold 0.000000 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.202 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.001537 / 0.006149 = 0.250 => 1 walker(s) + NFE : selection score for walker 2 is 0.001537 / 0.006149 = 0.250 => 1 walker(s) + NFE : selection score for walker 3 is 0.001537 / 0.006149 = 0.250 => 1 walker(s) + NFE : selection score for walker 4 is 0.001537 / 0.006149 = 0.250 => 1 walker(s) + NFE : Selection entropy 0.000000 is greater than threshold 0.000000 |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 242.12 PRESS = 0.0 - Etot = -8159.6657 EKtot = 1531.2514 EPtot = -9690.9171 - BOND = 31.4875 ANGLE = 66.6856 DIHED = 70.6564 - 1-4 NB = 35.9745 1-4 EEL = 536.9254 VDWAALS = 1800.6319 - EELEC = -12233.2783 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8130E-04 + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 308.05 PRESS = 0.0 + Etot = -8209.3146 EKtot = 1948.2060 EPtot = -10157.5205 + BOND = 33.8149 ANGLE = 59.8723 DIHED = 71.2879 + 1-4 NB = 35.6074 1-4 EEL = 545.7737 VDWAALS = 1439.7417 + EELEC = -12343.8574 EHBOND = 0.0000 RESTRAINT = 0.2391 + EAMBER (non-restraint) = -10157.7596 + Ewald error estimate: 0.1104E-04 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 263.75 PRESS = 0.0 - Etot = -8143.8822 EKtot = 1667.9863 EPtot = -9811.8684 - BOND = 28.9576 ANGLE = 73.1756 DIHED = 73.0137 - 1-4 NB = 32.2743 1-4 EEL = 533.2632 VDWAALS = 1778.7706 - EELEC = -12331.3235 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.6517E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.239 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 297.05 PRESS = 0.0 + Etot = -8211.8490 EKtot = 1878.6031 EPtot = -10090.4521 + BOND = 31.0312 ANGLE = 65.2697 DIHED = 73.9875 + 1-4 NB = 31.4588 1-4 EEL = 541.2030 VDWAALS = 1452.8271 + EELEC = -12286.5031 EHBOND = 0.0000 RESTRAINT = 0.2737 + EAMBER (non-restraint) = -10090.7258 + Ewald error estimate: 0.2367E-03 ------------------------------------------------------------------------------ - NFE : selection score for walker 1 is 0.044458 / 0.283216 = 0.157 => 0 walker(s) - NFE : selection score for walker 2 is 0.062112 / 0.283216 = 0.219 => 1 walker(s) - NFE : selection score for walker 3 is 0.062112 / 0.283216 = 0.219 => 1 walker(s) - NFE : selection score for walker 4 is 0.114533 / 0.283216 = 0.404 => 2 walker(s) - NFE : Selection entropy 0.063998 is greater than threshold 0.000000 - NFE : Selection resampling : new 1 comes from 2 - + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.274 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : selection score for walker 1 is 0.000653 / 0.002614 = 0.250 => 1 walker(s) + NFE : selection score for walker 2 is 0.000653 / 0.002614 = 0.250 => 1 walker(s) + NFE : selection score for walker 3 is 0.000653 / 0.002614 = 0.250 => 1 walker(s) + NFE : selection score for walker 4 is 0.000653 / 0.002614 = 0.250 => 1 walker(s) + NFE : Selection entropy 0.000000 is greater than threshold 0.000000 |Largest sphere to fit in unit cell has radius = 14.075 A V E R A G E S O V E R 50 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 262.96 PRESS = 0.0 - Etot = -8257.5874 EKtot = 1663.0031 EPtot = -9920.5905 - BOND = 29.4923 ANGLE = 63.1125 DIHED = 77.7998 - 1-4 NB = 33.1269 1-4 EEL = 539.6449 VDWAALS = 1601.7266 - EELEC = -12265.4935 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1759E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.72 PRESS = 0.0 + Etot = -8207.8207 EKtot = 1933.4452 EPtot = -10141.2659 + BOND = 29.7657 ANGLE = 61.3549 DIHED = 78.5318 + 1-4 NB = 33.0378 1-4 EEL = 542.5278 VDWAALS = 1431.5358 + EELEC = -12318.1369 EHBOND = 0.0000 RESTRAINT = 0.1172 + EAMBER (non-restraint) = -10141.3831 + Ewald error estimate: 0.1720E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 25.70 PRESS = 0.0 - Etot = 121.2844 EKtot = 162.5022 EPtot = 155.1670 - BOND = 4.0525 ANGLE = 5.3098 DIHED = 3.7806 - 1-4 NB = 1.9117 1-4 EEL = 2.5526 VDWAALS = 138.0559 - EELEC = 47.4457 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8735E-04 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.79 PRESS = 0.0 + Etot = 9.1848 EKtot = 23.9628 EPtot = 20.6578 + BOND = 4.0532 ANGLE = 4.1533 DIHED = 3.7907 + 1-4 NB = 1.8975 1-4 EEL = 2.7436 VDWAALS = 18.2635 + EELEC = 21.7673 EHBOND = 0.0000 RESTRAINT = 0.0833 + EAMBER (non-restraint) = 20.5745 + Ewald error estimate: 0.9764E-04 ------------------------------------------------------------------------------ @@ -380,56 +420,51 @@ NGLY 5. TIMINGS -------------------------------------------------------------------------------- -|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> -| Read coords time 0.01 ( 0.29% of Total) +| Read coords time 0.01 ( 0.36% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.13 (81.43% of List ) -| Other 0.03 (18.57% of List ) -| List time 0.17 (10.75% of Nonbo) -| Short_ene time 0.95 (98.34% of Direc) -| Other 0.02 ( 1.66% of Direc) -| Direct Ewald time 0.96 (70.15% of Ewald) -| Adjust Ewald time 0.01 ( 0.56% of Ewald) +| Build the list 0.16 (92.10% of List ) +| Other 0.01 ( 7.90% of List ) +| List time 0.17 (11.24% of Nonbo) +| Short_ene time 1.04 (99.10% of Direc) +| Other 0.01 ( 0.90% of Direc) +| Direct Ewald time 1.05 (76.93% of Ewald) +| Adjust Ewald time 0.01 ( 0.51% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 4.14% of Recip) -| Fill charge grid 0.02 ( 5.49% of Recip) -| Scalar sum 0.11 (28.28% of Recip) -| Grad sum 0.05 (11.77% of Recip) -| FFT back comm time 0.01 ( 6.53% of FFT t) -| Other 0.18 (93.47% of FFT t) -| FFT time 0.19 (50.10% of Recip) -| Other 0.00 ( 0.23% of Recip) -| Recip Ewald time 0.39 (28.27% of Ewald) -| Force Adjust 0.01 ( 0.83% of Ewald) -| Virial junk 0.00 ( 0.11% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 1.37 (89.25% of Nonbo) -| Nonbond force 1.54 (93.65% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.40% of Force) -| FRC Collect time 0.00 ( 0.15% of Force) -| Other 0.10 ( 5.79% of Force) -| Force time 1.64 (92.74% of Runmd) -| Shake time 0.01 ( 0.47% of Runmd) -| Verlet update time 0.08 ( 4.65% of Runmd) -| CRD distribute time 0.00 ( 0.09% of Runmd) -| Other 0.04 ( 2.05% of Runmd) -| Runmd Time 1.77 (95.07% of Total) -| Other 0.09 ( 4.63% of Total) -| Total time 1.86 (100.0% of ALL ) - -| Number of list builds : 5 - -| Highest rstack allocated: 146106 -| Highest istack allocated: 2444 +| Fill Bspline coeffs 0.01 ( 3.96% of Recip) +| Fill charge grid 0.02 ( 8.12% of Recip) +| Scalar sum 0.11 (35.82% of Recip) +| Grad sum 0.05 (17.86% of Recip) +| FFT back comm time 0.00 ( 0.01% of FFT t) +| Other 0.10 (100.0% of FFT t) +| FFT time 0.10 (34.22% of Recip) +| Other 0.00 ( 0.02% of Recip) +| Recip Ewald time 0.31 (22.42% of Ewald) +| Force Adjust 0.00 ( 0.02% of Ewald) +| Virial junk 0.00 ( 0.05% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.36 (88.76% of Nonbo) +| Nonbond force 1.54 (93.00% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.42% of Force) +| Other 0.11 ( 6.59% of Force) +| Force time 1.65 (96.19% of Runmd) +| Shake time 0.01 ( 0.45% of Runmd) +| Verlet update time 0.05 ( 3.04% of Runmd) +| Other 0.01 ( 0.32% of Runmd) +| Runmd Time 1.72 (97.70% of Total) +| Other 0.03 ( 1.93% of Total) +| Total time 1.76 (100.0% of ALL ) + +| Highest rstack allocated: 191619 +| Highest istack allocated: 3143 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 1.77 Per Step(ms) = 35.41 -| ns/day = 4.88 seconds/ns = 17702.96 +| Elapsed(s) = 1.72 Per Step(ms) = 34.36 +| ns/day = 5.03 seconds/ns = 17182.45 | ----------------------------------------------------- -| Job began at 14:01:49.375 on 04/10/2018 -| Setup done at 14:01:49.468 on 04/10/2018 -| Run done at 14:01:51.238 on 04/10/2018 -| wallclock() was called 2783 times +| Job began at 15:33:20.938 on 09/04/2018 +| Setup done at 15:33:20.979 on 09/04/2018 +| Run done at 15:33:22.697 on 09/04/2018 +| wallclock() was called 2683 times diff --git test/nfe/mwabmd/save.sander/mdout.2 test/nfe/mwabmd/save.sander/mdout.2 index c29fbc569f..c9071b4387 100644 --- test/nfe/mwabmd/save.sander/mdout.2 +++ test/nfe/mwabmd/save.sander/mdout.2 @@ -3,10 +3,10 @@ Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 04/10/2018 at 14:01:49 +| Run on 09/23/2018 at 18:11:22 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/mwabmd +| Executable path: /home/feng/amber_dev/amber/bin/sander.MPI +| Working directory: /home/feng/amber_dev/amber/test/nfe/mwabmd | Hostname: kili.physics.ncsu.edu [-O]verwriting output @@ -57,7 +57,7 @@ File Assignments: umbrella_file = 'umbrella.2.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.2.nc' @@ -214,7 +214,7 @@ NGLY NFE : selection algorithm parameters: NFE : NFE : selection_freq = 10 (0.0200 ps) - NFE : selection scoring constant = 0.010000 + NFE : selection scoring constant = 0.020000 NFE : selection criterion epsilon = 0.000000 NFE : NFE : () () () () () () () () () () () () () () () () () () () () () () () () @@ -234,127 +234,169 @@ NGLY | TOTAL SIZE OF NONBOND LIST = 651498 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 295.81 PRESS = 0.0 - Etot = -8386.6443 EKtot = 1870.7978 EPtot = -10257.4421 + Etot = -8386.6363 EKtot = 1870.7978 EPtot = -10257.4341 BOND = 21.9075 ANGLE = 68.0223 DIHED = 69.2843 1-4 NB = 32.7030 1-4 EEL = 521.1360 VDWAALS = 1390.4554 - EELEC = -12360.9506 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12360.9506 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10257.4421 Ewald error estimate: 0.2427E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 304.58 PRESS = 0.0 - Etot = -8388.8308 EKtot = 1926.2407 EPtot = -10315.0715 + Etot = -8388.8129 EKtot = 1926.2407 EPtot = -10315.0536 BOND = 22.6084 ANGLE = 77.7201 DIHED = 67.9834 1-4 NB = 30.4737 1-4 EEL = 521.1888 VDWAALS = 1371.7863 - EELEC = -12406.8323 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12406.8323 EHBOND = 0.0000 RESTRAINT = 0.0179 + EAMBER (non-restraint) = -10315.0715 Ewald error estimate: 0.1019E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 2 comes from 3 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 2 comes from 4 |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 243.74 PRESS = 0.0 - Etot = -8365.6613 EKtot = 1541.4590 EPtot = -9907.1203 - BOND = 32.9499 ANGLE = 64.8537 DIHED = 70.9677 - 1-4 NB = 32.3170 1-4 EEL = 524.8629 VDWAALS = 1400.8535 - EELEC = -12033.9250 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1210E-03 + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 + Etot = -8320.0172 EKtot = 1879.6571 EPtot = -10199.6743 + BOND = 25.7314 ANGLE = 67.7047 DIHED = 76.2864 + 1-4 NB = 31.4941 1-4 EEL = 535.0442 VDWAALS = 1359.5172 + EELEC = -12295.5101 EHBOND = 0.0000 RESTRAINT = 0.0576 + EAMBER (non-restraint) = -10199.7320 + Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 269.11 PRESS = 0.0 - Etot = -8356.3721 EKtot = 1701.9135 EPtot = -10058.2856 - BOND = 35.8997 ANGLE = 48.1083 DIHED = 73.1185 - 1-4 NB = 32.9824 1-4 EEL = 526.7209 VDWAALS = 1395.9179 - EELEC = -12171.0333 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1178E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.058 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 + Etot = -8311.8651 EKtot = 1892.0360 EPtot = -10203.9010 + BOND = 32.8322 ANGLE = 68.2453 DIHED = 72.8983 + 1-4 NB = 28.3884 1-4 EEL = 536.4092 VDWAALS = 1387.0687 + EELEC = -12329.8338 EHBOND = 0.0000 RESTRAINT = 0.0905 + EAMBER (non-restraint) = -10203.9916 + Ewald error estimate: 0.2635E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.091 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NFE : Selection resampling : new 2 comes from 1 |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 244.82 PRESS = 0.0 - Etot = -8273.5171 EKtot = 1548.3012 EPtot = -9821.8183 - BOND = 29.8736 ANGLE = 64.3048 DIHED = 80.6807 - 1-4 NB = 33.9449 1-4 EEL = 539.6456 VDWAALS = 1639.8888 - EELEC = -12210.1568 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.7917E-04 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 304.33 PRESS = 0.0 + Etot = -8214.7597 EKtot = 1924.6797 EPtot = -10139.4394 + BOND = 32.7375 ANGLE = 59.8108 DIHED = 81.8667 + 1-4 NB = 34.3189 1-4 EEL = 540.6806 VDWAALS = 1427.0107 + EELEC = -12315.9698 EHBOND = 0.0000 RESTRAINT = 0.1053 + EAMBER (non-restraint) = -10139.5446 + Ewald error estimate: 0.2810E-04 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 261.09 PRESS = 0.0 - Etot = -8266.3950 EKtot = 1651.2182 EPtot = -9917.6132 - BOND = 28.4962 ANGLE = 68.4539 DIHED = 77.3187 - 1-4 NB = 33.8932 1-4 EEL = 540.3890 VDWAALS = 1631.5061 - EELEC = -12297.6702 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1035E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.105 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 306.17 PRESS = 0.0 + Etot = -8217.6738 EKtot = 1936.3007 EPtot = -10153.9745 + BOND = 27.7620 ANGLE = 67.5250 DIHED = 80.3633 + 1-4 NB = 34.0498 1-4 EEL = 542.3720 VDWAALS = 1444.0653 + EELEC = -12350.2447 EHBOND = 0.0000 RESTRAINT = 0.1328 + EAMBER (non-restraint) = -10154.1073 + Ewald error estimate: 0.1700E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.133 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 2 comes from 1 + |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 241.91 PRESS = 0.0 - Etot = -8178.2283 EKtot = 1529.9024 EPtot = -9708.1307 - BOND = 31.5942 ANGLE = 70.1184 DIHED = 76.5854 - 1-4 NB = 32.9887 1-4 EEL = 544.2672 VDWAALS = 1737.3083 - EELEC = -12200.9929 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2704E-03 + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 298.82 PRESS = 0.0 + Etot = -8216.1590 EKtot = 1889.7927 EPtot = -10105.9517 + BOND = 29.0913 ANGLE = 68.4372 DIHED = 79.1987 + 1-4 NB = 32.9257 1-4 EEL = 547.9543 VDWAALS = 1460.4301 + EELEC = -12324.1567 EHBOND = 0.0000 RESTRAINT = 0.1677 + EAMBER (non-restraint) = -10106.1194 + Ewald error estimate: 0.3806E-03 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 270.60 PRESS = 0.0 - Etot = -8171.4158 EKtot = 1711.3364 EPtot = -9882.7522 - BOND = 33.1766 ANGLE = 63.0504 DIHED = 74.8656 - 1-4 NB = 34.5282 1-4 EEL = 539.9276 VDWAALS = 1712.9175 - EELEC = -12341.2179 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2643E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.168 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 303.32 PRESS = 0.0 + Etot = -8210.6219 EKtot = 1918.2364 EPtot = -10128.8584 + BOND = 33.3262 ANGLE = 62.2842 DIHED = 76.5199 + 1-4 NB = 34.6190 1-4 EEL = 544.8030 VDWAALS = 1451.2291 + EELEC = -12331.8415 EHBOND = 0.0000 RESTRAINT = 0.2018 + EAMBER (non-restraint) = -10129.0601 + Ewald error estimate: 0.2168E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.202 + BBMD : 0.000 STSM : 0.000 +=============================================================================== |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 241.44 PRESS = 0.0 - Etot = -8147.0574 EKtot = 1526.9222 EPtot = -9673.9796 - BOND = 33.3410 ANGLE = 64.7681 DIHED = 70.8020 - 1-4 NB = 35.6592 1-4 EEL = 540.2435 VDWAALS = 1813.4329 - EELEC = -12232.2262 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1703E-03 + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 308.05 PRESS = 0.0 + Etot = -8209.3146 EKtot = 1948.2060 EPtot = -10157.5205 + BOND = 33.8149 ANGLE = 59.8723 DIHED = 71.2879 + 1-4 NB = 35.6074 1-4 EEL = 545.7737 VDWAALS = 1439.7417 + EELEC = -12343.8574 EHBOND = 0.0000 RESTRAINT = 0.2391 + EAMBER (non-restraint) = -10157.7596 + Ewald error estimate: 0.1104E-04 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 265.09 PRESS = 0.0 - Etot = -8130.2184 EKtot = 1676.4654 EPtot = -9806.6838 - BOND = 29.2569 ANGLE = 69.7260 DIHED = 72.5416 - 1-4 NB = 31.8540 1-4 EEL = 535.6817 VDWAALS = 1786.0451 - EELEC = -12331.7890 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5746E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.239 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 297.05 PRESS = 0.0 + Etot = -8211.8490 EKtot = 1878.6031 EPtot = -10090.4521 + BOND = 31.0312 ANGLE = 65.2697 DIHED = 73.9875 + 1-4 NB = 31.4588 1-4 EEL = 541.2030 VDWAALS = 1452.8271 + EELEC = -12286.5031 EHBOND = 0.0000 RESTRAINT = 0.2737 + EAMBER (non-restraint) = -10090.7258 + Ewald error estimate: 0.2367E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 2 comes from 3 - + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.274 + BBMD : 0.000 STSM : 0.000 +=============================================================================== |Largest sphere to fit in unit cell has radius = 14.075 A V E R A G E S O V E R 50 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 256.60 PRESS = 0.0 - Etot = -8320.3012 EKtot = 1622.7758 EPtot = -9943.0770 - BOND = 28.5534 ANGLE = 65.7416 DIHED = 73.3446 - 1-4 NB = 33.2961 1-4 EEL = 533.4298 VDWAALS = 1577.0632 - EELEC = -12254.5057 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1666E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.56 PRESS = 0.0 + Etot = -8268.7117 EKtot = 1907.1103 EPtot = -10175.8221 + BOND = 28.4861 ANGLE = 66.2220 DIHED = 75.0881 + 1-4 NB = 33.1760 1-4 EEL = 537.7182 VDWAALS = 1416.0350 + EELEC = -12332.6654 EHBOND = 0.0000 RESTRAINT = 0.1178 + EAMBER (non-restraint) = -10175.9399 + Ewald error estimate: 0.1470E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 31.32 PRESS = 0.0 - Etot = 213.4585 EKtot = 198.1012 EPtot = 197.7426 - BOND = 3.3795 ANGLE = 6.4234 DIHED = 3.9915 - 1-4 NB = 1.5026 1-4 EEL = 8.6081 VDWAALS = 168.2498 - EELEC = 100.7700 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8482E-04 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 5.06 PRESS = 0.0 + Etot = 71.6275 EKtot = 32.0273 EPtot = 57.8345 + BOND = 3.5945 ANGLE = 5.1354 DIHED = 4.6523 + 1-4 NB = 1.8506 1-4 EEL = 9.0644 VDWAALS = 37.0952 + EELEC = 29.8480 EHBOND = 0.0000 RESTRAINT = 0.0836 + EAMBER (non-restraint) = 57.7509 + Ewald error estimate: 0.9746E-04 ------------------------------------------------------------------------------ @@ -363,41 +405,41 @@ NGLY -------------------------------------------------------------------------------- |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> -| Read coords time 0.01 ( 0.30% of Total) +| Read coords time 0.01 ( 0.29% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.15 (83.73% of List ) -| Other 0.03 (16.27% of List ) -| List time 0.18 (11.42% of Nonbo) -| Short_ene time 0.94 (98.31% of Direc) -| Other 0.02 ( 1.69% of Direc) -| Direct Ewald time 0.95 (69.92% of Ewald) +| Build the list 0.23 (89.13% of List ) +| Other 0.03 (10.87% of List ) +| List time 0.26 (16.36% of Nonbo) +| Short_ene time 0.92 (98.29% of Direc) +| Other 0.02 ( 1.71% of Direc) +| Direct Ewald time 0.94 (69.97% of Ewald) | Adjust Ewald time 0.01 ( 0.56% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 4.13% of Recip) -| Fill charge grid 0.02 ( 5.52% of Recip) -| Scalar sum 0.11 (28.35% of Recip) -| Grad sum 0.05 (11.75% of Recip) -| FFT back comm time 0.01 ( 5.93% of FFT t) -| Other 0.18 (94.07% of FFT t) -| FFT time 0.19 (49.91% of Recip) -| Other 0.00 ( 0.33% of Recip) -| Recip Ewald time 0.39 (28.40% of Ewald) -| Force Adjust 0.01 ( 0.93% of Ewald) -| Virial junk 0.00 ( 0.11% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 1.36 (88.58% of Nonbo) -| Nonbond force 1.54 (93.62% of Force) +| Fill Bspline coeffs 0.02 ( 4.25% of Recip) +| Fill charge grid 0.02 ( 5.72% of Recip) +| Scalar sum 0.11 (29.15% of Recip) +| Grad sum 0.05 (12.05% of Recip) +| FFT back comm time 0.01 ( 7.11% of FFT t) +| Other 0.17 (92.89% of FFT t) +| FFT time 0.18 (48.54% of Recip) +| Other 0.00 ( 0.30% of Recip) +| Recip Ewald time 0.38 (28.02% of Ewald) +| Force Adjust 0.02 ( 1.23% of Ewald) +| Virial junk 0.00 ( 0.12% of Ewald) +| Other 0.00 ( 0.09% of Ewald) +| Ewald time 1.34 (83.63% of Nonbo) +| Nonbond force 1.60 (94.47% of Force) | Bond/Angle/Dihedral 0.01 ( 0.42% of Force) -| FRC Collect time 0.00 ( 0.13% of Force) -| Other 0.10 ( 5.84% of Force) -| Force time 1.64 (93.31% of Runmd) -| Shake time 0.01 ( 0.47% of Runmd) -| Verlet update time 0.08 ( 4.69% of Runmd) -| CRD distribute time 0.00 ( 0.05% of Runmd) -| Other 0.03 ( 1.47% of Runmd) -| Runmd Time 1.76 (95.03% of Total) -| Other 0.09 ( 4.66% of Total) -| Total time 1.85 (100.0% of ALL ) +| FRC Collect time 0.00 ( 0.16% of Force) +| Other 0.08 ( 4.96% of Force) +| Force time 1.70 (91.99% of Runmd) +| Shake time 0.01 ( 0.45% of Runmd) +| Verlet update time 0.08 ( 4.49% of Runmd) +| CRD distribute time 0.00 ( 0.09% of Runmd) +| Other 0.06 ( 2.98% of Runmd) +| Runmd Time 1.84 (96.92% of Total) +| Other 0.05 ( 2.78% of Total) +| Total time 1.90 (98.63% of ALL ) | Number of list builds : 5 @@ -407,11 +449,11 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 1.76 Per Step(ms) = 35.17 -| ns/day = 4.91 seconds/ns = 17584.94 +| Elapsed(s) = 1.84 Per Step(ms) = 36.90 +| ns/day = 4.68 seconds/ns = 18449.60 | ----------------------------------------------------- -| Job began at 14:01:49.386 on 04/10/2018 -| Setup done at 14:01:49.480 on 04/10/2018 -| Run done at 14:01:51.238 on 04/10/2018 +| Job began at 18:11:22.574 on 09/23/2018 +| Setup done at 18:11:22.688 on 09/23/2018 +| Run done at 18:11:24.533 on 09/23/2018 | wallclock() was called 2783 times diff --git test/nfe/mwabmd/save.sander/mdout.3 test/nfe/mwabmd/save.sander/mdout.3 index 931619b4b1..40321b7ac7 100644 --- test/nfe/mwabmd/save.sander/mdout.3 +++ test/nfe/mwabmd/save.sander/mdout.3 @@ -3,10 +3,10 @@ Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 04/10/2018 at 14:01:49 +| Run on 09/23/2018 at 18:11:22 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/mwabmd +| Executable path: /home/feng/amber_dev/amber/bin/sander.MPI +| Working directory: /home/feng/amber_dev/amber/test/nfe/mwabmd | Hostname: kili.physics.ncsu.edu [-O]verwriting output @@ -57,7 +57,7 @@ File Assignments: umbrella_file = 'umbrella.3.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.3.nc' @@ -214,7 +214,7 @@ NGLY NFE : selection algorithm parameters: NFE : NFE : selection_freq = 10 (0.0200 ps) - NFE : selection scoring constant = 0.010000 + NFE : selection scoring constant = 0.020000 NFE : selection criterion epsilon = 0.000000 NFE : NFE : () () () () () () () () () () () () () () () () () () () () () () () () @@ -234,127 +234,169 @@ NGLY | TOTAL SIZE OF NONBOND LIST = 651110 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 298.58 PRESS = 0.0 - Etot = -8245.0626 EKtot = 1888.2779 EPtot = -10133.3405 + Etot = -8245.0546 EKtot = 1888.2779 EPtot = -10133.3326 BOND = 35.8447 ANGLE = 58.9315 DIHED = 71.9497 1-4 NB = 30.1714 1-4 EEL = 529.0876 VDWAALS = 1322.0722 - EELEC = -12181.3976 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12181.3976 EHBOND = 0.0000 RESTRAINT = 0.0080 + EAMBER (non-restraint) = -10133.3405 Ewald error estimate: 0.3303E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.008 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.08 PRESS = 0.0 - Etot = -8235.4665 EKtot = 1916.7738 EPtot = -10152.2403 + Etot = -8235.4486 EKtot = 1916.7738 EPtot = -10152.2224 BOND = 29.8765 ANGLE = 64.3672 DIHED = 72.3614 1-4 NB = 29.6021 1-4 EEL = 524.6812 VDWAALS = 1325.8059 - EELEC = -12198.9346 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12198.9346 EHBOND = 0.0000 RESTRAINT = 0.0179 + EAMBER (non-restraint) = -10152.2403 Ewald error estimate: 0.4081E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.018 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NFE : Selection resampling : new 3 comes from 4 |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 245.36 PRESS = 0.0 - Etot = -8448.3567 EKtot = 1551.7341 EPtot = -10000.0908 - BOND = 25.7927 ANGLE = 67.8571 DIHED = 76.1996 - 1-4 NB = 31.5373 1-4 EEL = 535.0891 VDWAALS = 1443.7324 - EELEC = -12180.2990 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1623E-03 + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 + Etot = -8320.0172 EKtot = 1879.6571 EPtot = -10199.6743 + BOND = 25.7314 ANGLE = 67.7047 DIHED = 76.2864 + 1-4 NB = 31.4941 1-4 EEL = 535.0442 VDWAALS = 1359.5172 + EELEC = -12295.5101 EHBOND = 0.0000 RESTRAINT = 0.0576 + EAMBER (non-restraint) = -10199.7320 + Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 268.95 PRESS = 0.0 - Etot = -8436.9480 EKtot = 1700.9343 EPtot = -10137.8822 - BOND = 33.4949 ANGLE = 68.1343 DIHED = 73.4014 - 1-4 NB = 28.6622 1-4 EEL = 536.6562 VDWAALS = 1473.8154 - EELEC = -12352.0464 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2513E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.058 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 + Etot = -8311.8651 EKtot = 1892.0360 EPtot = -10203.9010 + BOND = 32.8322 ANGLE = 68.2453 DIHED = 72.8983 + 1-4 NB = 28.3884 1-4 EEL = 536.4092 VDWAALS = 1387.0687 + EELEC = -12329.8338 EHBOND = 0.0000 RESTRAINT = 0.0905 + EAMBER (non-restraint) = -10203.9916 + Ewald error estimate: 0.2635E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.091 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 3 comes from 1 + |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 238.27 PRESS = 0.0 - Etot = -8431.8442 EKtot = 1506.8933 EPtot = -9938.7374 - BOND = 34.7864 ANGLE = 71.6861 DIHED = 74.9338 - 1-4 NB = 29.6518 1-4 EEL = 539.7685 VDWAALS = 1576.8864 - EELEC = -12266.4503 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1760E-03 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 304.33 PRESS = 0.0 + Etot = -8214.7597 EKtot = 1924.6797 EPtot = -10139.4394 + BOND = 32.7375 ANGLE = 59.8108 DIHED = 81.8667 + 1-4 NB = 34.3189 1-4 EEL = 540.6806 VDWAALS = 1427.0107 + EELEC = -12315.9698 EHBOND = 0.0000 RESTRAINT = 0.1053 + EAMBER (non-restraint) = -10139.5446 + Ewald error estimate: 0.2810E-04 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 258.85 PRESS = 0.0 - Etot = -8417.7410 EKtot = 1637.0234 EPtot = -10054.7644 - BOND = 32.9286 ANGLE = 64.4589 DIHED = 74.5152 - 1-4 NB = 31.5133 1-4 EEL = 536.8374 VDWAALS = 1567.8275 - EELEC = -12362.8454 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5376E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.105 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 306.17 PRESS = 0.0 + Etot = -8217.6738 EKtot = 1936.3007 EPtot = -10153.9745 + BOND = 27.7620 ANGLE = 67.5250 DIHED = 80.3633 + 1-4 NB = 34.0498 1-4 EEL = 542.3720 VDWAALS = 1444.0653 + EELEC = -12350.2447 EHBOND = 0.0000 RESTRAINT = 0.1328 + EAMBER (non-restraint) = -10154.1073 + Ewald error estimate: 0.1700E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.133 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 3 comes from 2 + |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 236.68 PRESS = 0.0 - Etot = -8354.0293 EKtot = 1496.8316 EPtot = -9850.8609 - BOND = 22.6980 ANGLE = 70.2821 DIHED = 74.2080 - 1-4 NB = 31.6591 1-4 EEL = 533.9548 VDWAALS = 1671.9847 - EELEC = -12255.6476 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.6258E-05 + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 298.82 PRESS = 0.0 + Etot = -8216.1590 EKtot = 1889.7927 EPtot = -10105.9517 + BOND = 29.0913 ANGLE = 68.4372 DIHED = 79.1987 + 1-4 NB = 32.9257 1-4 EEL = 547.9543 VDWAALS = 1460.4301 + EELEC = -12324.1567 EHBOND = 0.0000 RESTRAINT = 0.1677 + EAMBER (non-restraint) = -10106.1194 + Ewald error estimate: 0.3806E-03 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 260.50 PRESS = 0.0 - Etot = -8346.7401 EKtot = 1647.4380 EPtot = -9994.1781 - BOND = 26.9227 ANGLE = 61.2269 DIHED = 74.4652 - 1-4 NB = 36.2730 1-4 EEL = 534.3175 VDWAALS = 1663.2006 - EELEC = -12390.5839 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.9235E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.168 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 303.32 PRESS = 0.0 + Etot = -8210.6219 EKtot = 1918.2364 EPtot = -10128.8584 + BOND = 33.3262 ANGLE = 62.2842 DIHED = 76.5199 + 1-4 NB = 34.6190 1-4 EEL = 544.8030 VDWAALS = 1451.2291 + EELEC = -12331.8415 EHBOND = 0.0000 RESTRAINT = 0.2018 + EAMBER (non-restraint) = -10129.0601 + Ewald error estimate: 0.2168E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 3 comes from 2 - + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.202 + BBMD : 0.000 STSM : 0.000 +=============================================================================== |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 241.44 PRESS = 0.0 - Etot = -8147.0574 EKtot = 1526.9222 EPtot = -9673.9796 - BOND = 33.3410 ANGLE = 64.7681 DIHED = 70.8020 - 1-4 NB = 35.6592 1-4 EEL = 540.2435 VDWAALS = 1813.4329 - EELEC = -12232.2262 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1703E-03 + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 308.05 PRESS = 0.0 + Etot = -8209.3146 EKtot = 1948.2060 EPtot = -10157.5205 + BOND = 33.8149 ANGLE = 59.8723 DIHED = 71.2879 + 1-4 NB = 35.6074 1-4 EEL = 545.7737 VDWAALS = 1439.7417 + EELEC = -12343.8574 EHBOND = 0.0000 RESTRAINT = 0.2391 + EAMBER (non-restraint) = -10157.7596 + Ewald error estimate: 0.1104E-04 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 265.09 PRESS = 0.0 - Etot = -8130.2184 EKtot = 1676.4654 EPtot = -9806.6838 - BOND = 29.2569 ANGLE = 69.7260 DIHED = 72.5416 - 1-4 NB = 31.8540 1-4 EEL = 535.6817 VDWAALS = 1786.0451 - EELEC = -12331.7890 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5746E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.239 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 297.05 PRESS = 0.0 + Etot = -8211.8490 EKtot = 1878.6031 EPtot = -10090.4521 + BOND = 31.0312 ANGLE = 65.2697 DIHED = 73.9875 + 1-4 NB = 31.4588 1-4 EEL = 541.2030 VDWAALS = 1452.8271 + EELEC = -12286.5031 EHBOND = 0.0000 RESTRAINT = 0.2737 + EAMBER (non-restraint) = -10090.7258 + Ewald error estimate: 0.2367E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 3 comes from 4 - + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.274 + BBMD : 0.000 STSM : 0.000 +=============================================================================== |Largest sphere to fit in unit cell has radius = 14.075 A V E R A G E S O V E R 50 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 254.53 PRESS = 0.0 - Etot = -8373.7713 EKtot = 1609.6940 EPtot = -9983.4653 - BOND = 30.4050 ANGLE = 66.3683 DIHED = 73.8010 - 1-4 NB = 31.7033 1-4 EEL = 535.4269 VDWAALS = 1548.8689 - EELEC = -12270.0387 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1897E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 302.38 PRESS = 0.0 + Etot = -8240.0890 EKtot = 1912.3420 EPtot = -10152.4310 + BOND = 29.5088 ANGLE = 63.2785 DIHED = 75.9804 + 1-4 NB = 32.6802 1-4 EEL = 539.1765 VDWAALS = 1403.0515 + EELEC = -12296.2247 EHBOND = 0.0000 RESTRAINT = 0.1178 + EAMBER (non-restraint) = -10152.5488 + Ewald error estimate: 0.1971E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 33.18 PRESS = 0.0 - Etot = 220.9333 EKtot = 209.8262 EPtot = 154.2387 - BOND = 4.2094 ANGLE = 5.6323 DIHED = 2.0720 - 1-4 NB = 2.3218 1-4 EEL = 4.2609 VDWAALS = 166.5286 - EELEC = 65.8103 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1268E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.60 PRESS = 0.0 + Etot = 40.7759 EKtot = 22.7514 EPtot = 31.6669 + BOND = 3.5234 ANGLE = 4.9631 DIHED = 3.4233 + 1-4 NB = 2.2508 1-4 EEL = 6.5718 VDWAALS = 52.7469 + EELEC = 55.2544 EHBOND = 0.0000 RESTRAINT = 0.0836 + EAMBER (non-restraint) = 31.5833 + Ewald error estimate: 0.1303E-03 ------------------------------------------------------------------------------ @@ -363,41 +405,41 @@ NGLY -------------------------------------------------------------------------------- |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> -| Read coords time 0.01 ( 0.34% of Total) +| Read coords time 0.01 ( 0.29% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.14 (83.05% of List ) -| Other 0.03 (16.95% of List ) -| List time 0.17 (11.08% of Nonbo) -| Short_ene time 0.92 (98.30% of Direc) -| Other 0.02 ( 1.70% of Direc) -| Direct Ewald time 0.94 (68.99% of Ewald) -| Adjust Ewald time 0.01 ( 0.56% of Ewald) +| Build the list 0.14 (83.27% of List ) +| Other 0.03 (16.73% of List ) +| List time 0.17 (10.88% of Nonbo) +| Short_ene time 0.94 (98.31% of Direc) +| Other 0.02 ( 1.69% of Direc) +| Direct Ewald time 0.95 (68.02% of Ewald) +| Adjust Ewald time 0.01 ( 0.57% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 4.07% of Recip) -| Fill charge grid 0.02 ( 5.37% of Recip) -| Scalar sum 0.11 (27.73% of Recip) -| Grad sum 0.05 (11.40% of Recip) -| FFT back comm time 0.02 ( 7.92% of FFT t) -| Other 0.19 (92.08% of FFT t) -| FFT time 0.20 (51.21% of Recip) -| Other 0.00 ( 0.22% of Recip) -| Recip Ewald time 0.40 (29.10% of Ewald) -| Force Adjust 0.02 ( 1.15% of Ewald) -| Virial junk 0.00 ( 0.12% of Ewald) +| Fill Bspline coeffs 0.02 ( 3.92% of Recip) +| Fill charge grid 0.02 ( 5.22% of Recip) +| Scalar sum 0.11 (26.80% of Recip) +| Grad sum 0.05 (11.12% of Recip) +| FFT back comm time 0.01 ( 5.84% of FFT t) +| Other 0.20 (94.16% of FFT t) +| FFT time 0.22 (52.46% of Recip) +| Other 0.00 ( 0.48% of Recip) +| Recip Ewald time 0.41 (29.40% of Ewald) +| Force Adjust 0.03 ( 1.83% of Ewald) +| Virial junk 0.00 ( 0.11% of Ewald) | Other 0.00 ( 0.07% of Ewald) -| Ewald time 1.36 (88.92% of Nonbo) -| Nonbond force 1.53 (93.53% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.43% of Force) +| Ewald time 1.40 (89.11% of Nonbo) +| Nonbond force 1.57 (92.60% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.41% of Force) | FRC Collect time 0.00 ( 0.13% of Force) -| Other 0.10 ( 5.91% of Force) -| Force time 1.64 (93.88% of Runmd) -| Shake time 0.01 ( 0.48% of Runmd) -| Verlet update time 0.08 ( 4.78% of Runmd) +| Other 0.12 ( 6.86% of Force) +| Force time 1.70 (92.10% of Runmd) +| Shake time 0.01 ( 0.45% of Runmd) +| Verlet update time 0.08 ( 4.48% of Runmd) | CRD distribute time 0.00 ( 0.05% of Runmd) -| Other 0.01 ( 0.81% of Runmd) -| Runmd Time 1.75 (93.79% of Total) -| Other 0.11 ( 5.86% of Total) -| Total time 1.86 (100.0% of ALL ) +| Other 0.05 ( 2.92% of Runmd) +| Runmd Time 1.84 (94.20% of Total) +| Other 0.11 ( 5.50% of Total) +| Total time 1.96 (100.0% of ALL ) | Number of list builds : 5 @@ -407,11 +449,11 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 1.75 Per Step(ms) = 34.91 -| ns/day = 4.95 seconds/ns = 17457.11 +| Elapsed(s) = 1.84 Per Step(ms) = 36.90 +| ns/day = 4.68 seconds/ns = 18449.12 | ----------------------------------------------------- -| Job began at 14:01:49.375 on 04/10/2018 -| Setup done at 14:01:49.493 on 04/10/2018 -| Run done at 14:01:51.238 on 04/10/2018 +| Job began at 18:11:22.574 on 09/23/2018 +| Setup done at 18:11:22.688 on 09/23/2018 +| Run done at 18:11:24.533 on 09/23/2018 | wallclock() was called 2783 times diff --git test/nfe/mwabmd/save.sander/mdout.4 test/nfe/mwabmd/save.sander/mdout.4 index 71c0a425d9..798437f9c8 100644 --- test/nfe/mwabmd/save.sander/mdout.4 +++ test/nfe/mwabmd/save.sander/mdout.4 @@ -3,10 +3,10 @@ Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 04/10/2018 at 14:01:49 +| Run on 09/23/2018 at 18:11:22 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/mwabmd +| Executable path: /home/feng/amber_dev/amber/bin/sander.MPI +| Working directory: /home/feng/amber_dev/amber/test/nfe/mwabmd | Hostname: kili.physics.ncsu.edu [-O]verwriting output @@ -57,7 +57,7 @@ File Assignments: umbrella_file = 'umbrella.4.nc' selection_freq = 10 - selection_constant = 0.01 + selection_constant = 0.02 wt_temperature = 10000.0 wt_umbrella_file = 'wt_umbrella.4.nc' @@ -214,7 +214,7 @@ NGLY NFE : selection algorithm parameters: NFE : NFE : selection_freq = 10 (0.0200 ps) - NFE : selection scoring constant = 0.010000 + NFE : selection scoring constant = 0.020000 NFE : selection criterion epsilon = 0.000000 NFE : NFE : () () () () () () () () () () () () () () () () () () () () () () () () @@ -234,123 +234,167 @@ NGLY | TOTAL SIZE OF NONBOND LIST = 650668 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.4833 EKtot = 1914.1824 EPtot = -10235.6657 + Etot = -8321.4710 EKtot = 1914.1824 EPtot = -10235.6534 BOND = 19.0734 ANGLE = 63.5926 DIHED = 72.6962 1-4 NB = 31.9325 1-4 EEL = 541.0002 VDWAALS = 1297.2732 - EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0123 + EAMBER (non-restraint) = -10235.6657 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.012 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.15 PRESS = 0.0 - Etot = -8329.3298 EKtot = 1917.1639 EPtot = -10246.4937 + Etot = -8329.3030 EKtot = 1917.1639 EPtot = -10246.4669 BOND = 25.2751 ANGLE = 68.1066 DIHED = 73.1043 1-4 NB = 34.0178 1-4 EEL = 541.6435 VDWAALS = 1326.2609 - EELEC = -12314.9019 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9019 EHBOND = 0.0000 RESTRAINT = 0.0268 + EAMBER (non-restraint) = -10246.4937 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.027 + BBMD : 0.000 STSM : 0.000 +=============================================================================== |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 245.36 PRESS = 0.0 - Etot = -8448.3567 EKtot = 1551.7341 EPtot = -10000.0908 - BOND = 25.7927 ANGLE = 67.8571 DIHED = 76.1996 - 1-4 NB = 31.5373 1-4 EEL = 535.0891 VDWAALS = 1443.7324 - EELEC = -12180.2990 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1623E-03 + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 + Etot = -8320.0172 EKtot = 1879.6571 EPtot = -10199.6743 + BOND = 25.7314 ANGLE = 67.7047 DIHED = 76.2864 + 1-4 NB = 31.4941 1-4 EEL = 535.0442 VDWAALS = 1359.5172 + EELEC = -12295.5101 EHBOND = 0.0000 RESTRAINT = 0.0576 + EAMBER (non-restraint) = -10199.7320 + Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 268.95 PRESS = 0.0 - Etot = -8436.9480 EKtot = 1700.9343 EPtot = -10137.8822 - BOND = 33.4949 ANGLE = 68.1343 DIHED = 73.4014 - 1-4 NB = 28.6622 1-4 EEL = 536.6562 VDWAALS = 1473.8154 - EELEC = -12352.0464 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2513E-03 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.058 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.17 PRESS = 0.0 + Etot = -8311.8651 EKtot = 1892.0360 EPtot = -10203.9010 + BOND = 32.8322 ANGLE = 68.2453 DIHED = 72.8983 + 1-4 NB = 28.3884 1-4 EEL = 536.4092 VDWAALS = 1387.0687 + EELEC = -12329.8338 EHBOND = 0.0000 RESTRAINT = 0.0905 + EAMBER (non-restraint) = -10203.9916 + Ewald error estimate: 0.2635E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.091 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 4 comes from 2 + |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 238.27 PRESS = 0.0 - Etot = -8431.8442 EKtot = 1506.8933 EPtot = -9938.7374 - BOND = 34.7864 ANGLE = 71.6861 DIHED = 74.9338 - 1-4 NB = 29.6518 1-4 EEL = 539.7685 VDWAALS = 1576.8864 - EELEC = -12266.4503 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1760E-03 + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.81 PRESS = 0.0 + Etot = -8313.4691 EKtot = 1908.6890 EPtot = -10222.1581 + BOND = 35.4495 ANGLE = 70.8442 DIHED = 73.4768 + 1-4 NB = 28.8860 1-4 EEL = 538.8792 VDWAALS = 1406.8403 + EELEC = -12376.6460 EHBOND = 0.0000 RESTRAINT = 0.1119 + EAMBER (non-restraint) = -10222.2700 + Ewald error estimate: 0.3060E-04 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 258.85 PRESS = 0.0 - Etot = -8417.7410 EKtot = 1637.0234 EPtot = -10054.7644 - BOND = 32.9286 ANGLE = 64.4589 DIHED = 74.5152 - 1-4 NB = 31.5133 1-4 EEL = 536.8374 VDWAALS = 1567.8275 - EELEC = -12362.8454 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5376E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.112 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.89 PRESS = 0.0 + Etot = -8308.0017 EKtot = 1947.1702 EPtot = -10255.1719 + BOND = 32.8681 ANGLE = 64.4530 DIHED = 74.4285 + 1-4 NB = 30.2000 1-4 EEL = 534.5115 VDWAALS = 1408.1052 + EELEC = -12399.8637 EHBOND = 0.0000 RESTRAINT = 0.1254 + EAMBER (non-restraint) = -10255.2973 + Ewald error estimate: 0.7443E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.125 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + NFE : Selection resampling : new 4 comes from 3 + |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 236.68 PRESS = 0.0 - Etot = -8354.0293 EKtot = 1496.8316 EPtot = -9850.8609 - BOND = 22.6980 ANGLE = 70.2821 DIHED = 74.2080 - 1-4 NB = 31.6591 1-4 EEL = 533.9548 VDWAALS = 1671.9847 - EELEC = -12255.6476 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.6258E-05 + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 298.82 PRESS = 0.0 + Etot = -8216.1590 EKtot = 1889.7927 EPtot = -10105.9517 + BOND = 29.0913 ANGLE = 68.4372 DIHED = 79.1987 + 1-4 NB = 32.9257 1-4 EEL = 547.9543 VDWAALS = 1460.4301 + EELEC = -12324.1567 EHBOND = 0.0000 RESTRAINT = 0.1677 + EAMBER (non-restraint) = -10106.1194 + Ewald error estimate: 0.3806E-03 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 260.50 PRESS = 0.0 - Etot = -8346.7401 EKtot = 1647.4380 EPtot = -9994.1781 - BOND = 26.9227 ANGLE = 61.2269 DIHED = 74.4652 - 1-4 NB = 36.2730 1-4 EEL = 534.3175 VDWAALS = 1663.2006 - EELEC = -12390.5839 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.9235E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.168 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 303.32 PRESS = 0.0 + Etot = -8210.6219 EKtot = 1918.2364 EPtot = -10128.8584 + BOND = 33.3262 ANGLE = 62.2842 DIHED = 76.5199 + 1-4 NB = 34.6190 1-4 EEL = 544.8030 VDWAALS = 1451.2291 + EELEC = -12331.8415 EHBOND = 0.0000 RESTRAINT = 0.2018 + EAMBER (non-restraint) = -10129.0601 + Ewald error estimate: 0.2168E-03 ------------------------------------------------------------------------------ - NFE : Selection resampling : new 4 comes from 3 - + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.202 + BBMD : 0.000 STSM : 0.000 +=============================================================================== |Largest sphere to fit in unit cell has radius = 14.075 - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 233.64 PRESS = 0.0 - Etot = -8297.9482 EKtot = 1477.5816 EPtot = -9775.5298 - BOND = 29.0370 ANGLE = 59.5919 DIHED = 73.4226 - 1-4 NB = 36.9769 1-4 EEL = 537.1591 VDWAALS = 1757.8926 - EELEC = -12269.6099 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1745E-04 + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 308.05 PRESS = 0.0 + Etot = -8209.3146 EKtot = 1948.2060 EPtot = -10157.5205 + BOND = 33.8149 ANGLE = 59.8723 DIHED = 71.2879 + 1-4 NB = 35.6074 1-4 EEL = 545.7737 VDWAALS = 1439.7417 + EELEC = -12343.8574 EHBOND = 0.0000 RESTRAINT = 0.2391 + EAMBER (non-restraint) = -10157.7596 + Ewald error estimate: 0.1104E-04 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 255.62 PRESS = 0.0 - Etot = -8293.4102 EKtot = 1616.6310 EPtot = -9910.0412 - BOND = 23.0899 ANGLE = 69.2577 DIHED = 71.8253 - 1-4 NB = 36.2186 1-4 EEL = 539.2188 VDWAALS = 1709.0154 - EELEC = -12358.6669 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1415E-04 + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.239 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 297.05 PRESS = 0.0 + Etot = -8211.8490 EKtot = 1878.6031 EPtot = -10090.4521 + BOND = 31.0312 ANGLE = 65.2697 DIHED = 73.9875 + 1-4 NB = 31.4588 1-4 EEL = 541.2030 VDWAALS = 1452.8271 + EELEC = -12286.5031 EHBOND = 0.0000 RESTRAINT = 0.2737 + EAMBER (non-restraint) = -10090.7258 + Ewald error estimate: 0.2367E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.000 ABMD : 0.274 + BBMD : 0.000 STSM : 0.000 +=============================================================================== |Largest sphere to fit in unit cell has radius = 14.075 A V E R A G E S O V E R 50 S T E P S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 256.38 PRESS = 0.0 - Etot = -8398.8268 EKtot = 1621.4114 EPtot = -10020.2382 - BOND = 28.7523 ANGLE = 67.3645 DIHED = 73.9186 - 1-4 NB = 32.7514 1-4 EEL = 537.6462 VDWAALS = 1532.6604 - EELEC = -12293.3317 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1800E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 302.08 PRESS = 0.0 + Etot = -8275.6256 EKtot = 1910.4237 EPtot = -10186.0493 + BOND = 29.5087 ANGLE = 66.5270 DIHED = 74.7402 + 1-4 NB = 32.2430 1-4 EEL = 541.1290 VDWAALS = 1393.1990 + EELEC = -12323.5160 EHBOND = 0.0000 RESTRAINT = 0.1198 + EAMBER (non-restraint) = -10186.1691 + Ewald error estimate: 0.2103E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 25.79 PRESS = 0.0 - Etot = 118.0714 EKtot = 163.0867 EPtot = 150.5359 - BOND = 4.7233 ANGLE = 4.2407 DIHED = 2.0474 - 1-4 NB = 2.6192 1-4 EEL = 2.7789 VDWAALS = 157.2274 - EELEC = 55.9229 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1713E-03 + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.54 PRESS = 0.0 + Etot = 52.2997 EKtot = 22.4006 EPtot = 49.2015 + BOND = 3.8247 ANGLE = 4.4406 DIHED = 2.7374 + 1-4 NB = 2.3097 1-4 EEL = 3.9909 VDWAALS = 58.3474 + EELEC = 38.5794 EHBOND = 0.0000 RESTRAINT = 0.0821 + EAMBER (non-restraint) = 49.1194 + Ewald error estimate: 0.1591E-03 ------------------------------------------------------------------------------ @@ -359,41 +403,41 @@ NGLY -------------------------------------------------------------------------------- |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> -| Read coords time 0.01 ( 0.30% of Total) +| Read coords time 0.01 ( 0.29% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.14 (82.92% of List ) -| Other 0.03 (17.08% of List ) -| List time 0.17 (10.94% of Nonbo) -| Short_ene time 0.94 (98.32% of Direc) -| Other 0.02 ( 1.68% of Direc) -| Direct Ewald time 0.95 (69.48% of Ewald) -| Adjust Ewald time 0.01 ( 0.55% of Ewald) +| Build the list 0.17 (85.55% of List ) +| Other 0.03 (14.45% of List ) +| List time 0.20 (12.39% of Nonbo) +| Short_ene time 0.95 (98.25% of Direc) +| Other 0.02 ( 1.75% of Direc) +| Direct Ewald time 0.97 (69.11% of Ewald) +| Adjust Ewald time 0.01 ( 0.58% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 4.18% of Recip) -| Fill charge grid 0.02 ( 5.46% of Recip) -| Scalar sum 0.11 (28.19% of Recip) -| Grad sum 0.05 (11.66% of Recip) -| FFT back comm time 0.01 ( 7.17% of FFT t) -| Other 0.18 (92.83% of FFT t) -| FFT time 0.19 (49.89% of Recip) -| Other 0.00 ( 0.61% of Recip) -| Recip Ewald time 0.39 (28.55% of Ewald) -| Force Adjust 0.02 ( 1.23% of Ewald) -| Virial junk 0.00 ( 0.12% of Ewald) +| Fill Bspline coeffs 0.02 ( 4.12% of Recip) +| Fill charge grid 0.02 ( 5.41% of Recip) +| Scalar sum 0.11 (27.80% of Recip) +| Grad sum 0.05 (11.58% of Recip) +| FFT back comm time 0.02 ( 8.17% of FFT t) +| Other 0.18 (91.83% of FFT t) +| FFT time 0.20 (50.36% of Recip) +| Other 0.00 ( 0.73% of Recip) +| Recip Ewald time 0.40 (28.50% of Ewald) +| Force Adjust 0.02 ( 1.63% of Ewald) +| Virial junk 0.00 ( 0.11% of Ewald) | Other 0.00 ( 0.07% of Ewald) -| Ewald time 1.37 (89.05% of Nonbo) -| Nonbond force 1.54 (93.80% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.41% of Force) -| FRC Collect time 0.00 ( 0.14% of Force) -| Other 0.09 ( 5.65% of Force) -| Force time 1.64 (93.90% of Runmd) -| Shake time 0.01 ( 0.48% of Runmd) -| Verlet update time 0.08 ( 4.81% of Runmd) -| CRD distribute time 0.00 ( 0.10% of Runmd) -| Other 0.01 ( 0.70% of Runmd) -| Runmd Time 1.75 (94.28% of Total) -| Other 0.10 ( 5.41% of Total) -| Total time 1.85 (100.0% of ALL ) +| Ewald time 1.40 (87.61% of Nonbo) +| Nonbond force 1.60 (93.95% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.40% of Force) +| FRC Collect time 0.00 ( 0.13% of Force) +| Other 0.09 ( 5.53% of Force) +| Force time 1.70 (94.20% of Runmd) +| Shake time 0.01 ( 0.46% of Runmd) +| Verlet update time 0.08 ( 4.62% of Runmd) +| CRD distribute time 0.00 ( 0.05% of Runmd) +| Other 0.01 ( 0.67% of Runmd) +| Runmd Time 1.80 (96.24% of Total) +| Other 0.06 ( 3.46% of Total) +| Total time 1.87 (97.16% of ALL ) | Number of list builds : 5 @@ -403,11 +447,11 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 1.75 Per Step(ms) = 34.91 -| ns/day = 4.95 seconds/ns = 17457.03 +| Elapsed(s) = 1.80 Per Step(ms) = 36.09 +| ns/day = 4.79 seconds/ns = 18046.13 | ----------------------------------------------------- -| Job began at 14:01:49.385 on 04/10/2018 -| Setup done at 14:01:49.493 on 04/10/2018 -| Run done at 14:01:51.238 on 04/10/2018 +| Job began at 18:11:22.574 on 09/23/2018 +| Setup done at 18:11:22.728 on 09/23/2018 +| Run done at 18:11:24.533 on 09/23/2018 | wallclock() was called 2783 times diff --git test/nfe/mwabmd/save.sander/umbrella.1.ncdump test/nfe/mwabmd/save.sander/umbrella.1.ncdump new file mode 100644 index 0000000000..50725ca804 --- /dev/null +++ test/nfe/mwabmd/save.sander/umbrella.1.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0502425533, 0.2579158286, 0.3393774594, + 0.1844807562, 0.0618658170, 0.0003049922, 0.0000000000, + 0.0000000000, 0.0008648204, 0.0164693435, 0.0229234400, + 0.0096243675, 0.0000000000, 0.0043973768, 0.0205066390, + 0.0206277057, 0.0045667847, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.sander/umbrella.2.ncdump test/nfe/mwabmd/save.sander/umbrella.2.ncdump new file mode 100644 index 0000000000..50725ca804 --- /dev/null +++ test/nfe/mwabmd/save.sander/umbrella.2.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0502425533, 0.2579158286, 0.3393774594, + 0.1844807562, 0.0618658170, 0.0003049922, 0.0000000000, + 0.0000000000, 0.0008648204, 0.0164693435, 0.0229234400, + 0.0096243675, 0.0000000000, 0.0043973768, 0.0205066390, + 0.0206277057, 0.0045667847, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.sander/umbrella.3.ncdump test/nfe/mwabmd/save.sander/umbrella.3.ncdump new file mode 100644 index 0000000000..50725ca804 --- /dev/null +++ test/nfe/mwabmd/save.sander/umbrella.3.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0502425533, 0.2579158286, 0.3393774594, + 0.1844807562, 0.0618658170, 0.0003049922, 0.0000000000, + 0.0000000000, 0.0008648204, 0.0164693435, 0.0229234400, + 0.0096243675, 0.0000000000, 0.0043973768, 0.0205066390, + 0.0206277057, 0.0045667847, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.sander/umbrella.4.ncdump test/nfe/mwabmd/save.sander/umbrella.4.ncdump new file mode 100644 index 0000000000..50725ca804 --- /dev/null +++ test/nfe/mwabmd/save.sander/umbrella.4.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0502425533, 0.2579158286, 0.3393774594, + 0.1844807562, 0.0618658170, 0.0003049922, 0.0000000000, + 0.0000000000, 0.0008648204, 0.0164693435, 0.0229234400, + 0.0096243675, 0.0000000000, 0.0043973768, 0.0205066390, + 0.0206277057, 0.0045667847, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.sander/wt_umbrella.1.ncdump test/nfe/mwabmd/save.sander/wt_umbrella.1.ncdump new file mode 100644 index 0000000000..2d5e490eee --- /dev/null +++ test/nfe/mwabmd/save.sander/wt_umbrella.1.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0517498299, 0.2656533035, 0.3495587832, + 0.1900151789, 0.0637217915, 0.0003141419, 0.0000000000, + 0.0000000000, 0.0008907650, 0.0169634238, 0.0236111432, + 0.0099130985, 0.0000000000, 0.0045292981, 0.0211218382, + 0.0212465369, 0.0047037883, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.sander/wt_umbrella.2.ncdump test/nfe/mwabmd/save.sander/wt_umbrella.2.ncdump new file mode 100644 index 0000000000..2d5e490eee --- /dev/null +++ test/nfe/mwabmd/save.sander/wt_umbrella.2.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0517498299, 0.2656533035, 0.3495587832, + 0.1900151789, 0.0637217915, 0.0003141419, 0.0000000000, + 0.0000000000, 0.0008907650, 0.0169634238, 0.0236111432, + 0.0099130985, 0.0000000000, 0.0045292981, 0.0211218382, + 0.0212465369, 0.0047037883, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.sander/wt_umbrella.3.ncdump test/nfe/mwabmd/save.sander/wt_umbrella.3.ncdump new file mode 100644 index 0000000000..2d5e490eee --- /dev/null +++ test/nfe/mwabmd/save.sander/wt_umbrella.3.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0517498299, 0.2656533035, 0.3495587832, + 0.1900151789, 0.0637217915, 0.0003141419, 0.0000000000, + 0.0000000000, 0.0008907650, 0.0169634238, 0.0236111432, + 0.0099130985, 0.0000000000, 0.0045292981, 0.0211218382, + 0.0212465369, 0.0047037883, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/mwabmd/save.sander/wt_umbrella.4.ncdump test/nfe/mwabmd/save.sander/wt_umbrella.4.ncdump new file mode 100644 index 0000000000..2d5e490eee --- /dev/null +++ test/nfe/mwabmd/save.sander/wt_umbrella.4.ncdump @@ -0,0 +1,41 @@ +netcdf ncdump { +dimensions: + row-major = 97 ; +variables: + double coeffs(row-major) ; + coeffs:C_format = "%14.10f" ; + +// global attributes: + :nextents = 1 ; + :extents = 97 ; + :periodicity = 0 ; + :origin = 0. ; + :spacing = 0.125 ; +data: + + coeffs = 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0517498299, 0.2656533035, 0.3495587832, + 0.1900151789, 0.0637217915, 0.0003141419, 0.0000000000, + 0.0000000000, 0.0008907650, 0.0169634238, 0.0236111432, + 0.0099130985, 0.0000000000, 0.0045292981, 0.0211218382, + 0.0212465369, 0.0047037883, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000, 0.0000000000, 0.0000000000, 0.0000000000, + 0.0000000000 ; +} diff --git test/nfe/pmd/run-pmemd.sh test/nfe/pmd/run-pmemd.sh index 2d6dedcb1b..6bb4617c23 100755 --- test/nfe/pmd/run-pmemd.sh +++ test/nfe/pmd/run-pmemd.sh @@ -28,7 +28,7 @@ cp -p ../inpcrd.4 ./inpcrd # run SANDER # -${SANDER_CMD} > sander.out 2>&1 +${SANDER_CMD} -O > sander.out 2>&1 ../../dacdif -t 1 save.pmemd/mdout mdout ../../dacdif -t 1 save.pmemd/pmd.txt pmd.txt diff --git test/nfe/pmd/run-sander.sh test/nfe/pmd/run-sander.sh index ab42ffe529..a59bbcd2b4 100755 --- test/nfe/pmd/run-sander.sh +++ test/nfe/pmd/run-sander.sh @@ -28,7 +28,7 @@ cp -p ../inpcrd.4 ./inpcrd # run SANDER # -${SANDER_CMD} > sander.out 2>&1 +${SANDER_CMD} -O > sander.out 2>&1 ../../dacdif -t 1 save.sander/mdout mdout ../../dacdif -t 1 save.sander/pmd.txt pmd.txt diff --git test/nfe/pmd/save.pmemd/mdout test/nfe/pmd/save.pmemd/mdout index f1514fcd01..d2109c2257 100644 --- test/nfe/pmd/save.pmemd/mdout +++ test/nfe/pmd/save.pmemd/mdout @@ -1,15 +1,17 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 01/18/2017 at 09:14:19 +| Run on 09/05/2018 at 13:01:11 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/pmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/pmd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output File Assignments: | MDIN: mdin @@ -161,7 +163,7 @@ NGLY | Dynamic Memory, Types Used: | Reals 239932 -| Integers 196502 +| Integers 206014 | Nonbonded Pairs Initial Allocation: 179151 @@ -238,103 +240,144 @@ NGLY NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.5188 EKtot = 1914.1465 EPtot = -10235.6653 + Etot = -8321.2195 EKtot = 1914.1465 EPtot = -10235.3660 BOND = 19.0663 ANGLE = 63.5971 DIHED = 72.6948 1-4 NB = 31.9335 1-4 EEL = 541.0087 VDWAALS = 1297.2725 - EELEC = -12261.2382 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2382 EHBOND = 0.0000 RESTRAINT = 0.2993 + EAMBER (non-restraint) = -10235.6653 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.299 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.14 PRESS = 0.0 - Etot = -8329.4106 EKtot = 1917.1217 EPtot = -10246.5323 + Etot = -8329.0697 EKtot = 1917.1217 EPtot = -10246.1914 BOND = 25.2397 ANGLE = 68.0814 DIHED = 73.1111 1-4 NB = 34.0214 1-4 EEL = 541.6821 VDWAALS = 1326.2580 - EELEC = -12314.9261 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9261 EHBOND = 0.0000 RESTRAINT = 0.3410 + EAMBER (non-restraint) = -10246.5323 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.341 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.20 PRESS = 0.0 - Etot = -8320.1632 EKtot = 1879.5929 EPtot = -10199.7561 + Etot = -8319.8177 EKtot = 1879.5929 EPtot = -10199.4106 BOND = 25.7019 ANGLE = 67.6557 DIHED = 76.3006 1-4 NB = 31.5105 1-4 EEL = 535.1205 VDWAALS = 1359.5128 - EELEC = -12295.5581 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12295.5581 EHBOND = 0.0000 RESTRAINT = 0.3455 + EAMBER (non-restraint) = -10199.7561 Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.345 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.16 PRESS = 0.0 - Etot = -8312.0451 EKtot = 1891.9709 EPtot = -10204.0160 + Etot = -8311.7006 EKtot = 1891.9709 EPtot = -10203.6715 BOND = 32.7904 ANGLE = 68.1904 DIHED = 72.9052 1-4 NB = 28.4265 1-4 EEL = 536.5292 VDWAALS = 1387.0497 - EELEC = -12329.9074 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12329.9074 EHBOND = 0.0000 RESTRAINT = 0.3445 + EAMBER (non-restraint) = -10204.0160 Ewald error estimate: 0.2698E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.345 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.79 PRESS = 0.0 - Etot = -8313.6990 EKtot = 1908.6139 EPtot = -10222.3129 + Etot = -8313.3394 EKtot = 1908.6139 EPtot = -10221.9533 BOND = 35.3907 ANGLE = 70.7942 DIHED = 73.4732 1-4 NB = 28.9331 1-4 EEL = 539.0462 VDWAALS = 1406.8022 - EELEC = -12376.7525 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12376.7525 EHBOND = 0.0000 RESTRAINT = 0.3596 + EAMBER (non-restraint) = -10222.3129 Ewald error estimate: 0.3145E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.360 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.88 PRESS = 0.0 - Etot = -8308.2644 EKtot = 1947.0813 EPtot = -10255.3457 + Etot = -8307.8807 EKtot = 1947.0813 EPtot = -10254.9620 BOND = 32.7694 ANGLE = 64.3710 DIHED = 74.4239 1-4 NB = 30.2552 1-4 EEL = 534.7202 VDWAALS = 1408.1058 - EELEC = -12399.9912 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12399.9912 EHBOND = 0.0000 RESTRAINT = 0.3837 + EAMBER (non-restraint) = -10255.3457 Ewald error estimate: 0.7653E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.384 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 295.99 PRESS = 0.0 - Etot = -8312.4601 EKtot = 1871.9225 EPtot = -10184.3826 + Etot = -8312.0834 EKtot = 1871.9225 EPtot = -10184.0059 BOND = 23.7048 ANGLE = 70.7963 DIHED = 73.5110 1-4 NB = 30.2050 1-4 EEL = 531.3801 VDWAALS = 1412.1586 - EELEC = -12326.1383 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12326.1383 EHBOND = 0.0000 RESTRAINT = 0.3767 + EAMBER (non-restraint) = -10184.3826 Ewald error estimate: 0.7180E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.377 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.06 PRESS = 0.0 - Etot = -8316.4360 EKtot = 1897.6776 EPtot = -10214.1136 + Etot = -8316.0627 EKtot = 1897.6776 EPtot = -10213.7403 BOND = 27.5475 ANGLE = 63.4108 DIHED = 74.6817 1-4 NB = 34.6278 1-4 EEL = 531.2967 VDWAALS = 1411.0707 - EELEC = -12356.7488 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12356.7488 EHBOND = 0.0000 RESTRAINT = 0.3733 + EAMBER (non-restraint) = -10214.1136 Ewald error estimate: 0.2753E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.373 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 298.93 PRESS = 0.0 - Etot = -8320.8144 EKtot = 1890.4910 EPtot = -10211.3054 + Etot = -8320.4383 EKtot = 1890.4910 EPtot = -10210.9293 BOND = 28.9803 ANGLE = 59.0628 DIHED = 74.5811 1-4 NB = 35.6516 1-4 EEL = 533.4882 VDWAALS = 1407.9501 - EELEC = -12351.0195 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12351.0195 EHBOND = 0.0000 RESTRAINT = 0.3761 + EAMBER (non-restraint) = -10211.3054 Ewald error estimate: 0.1509E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.376 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.25 PRESS = 0.0 - Etot = -8323.5586 EKtot = 1930.4950 EPtot = -10254.0536 + Etot = -8323.1979 EKtot = 1930.4950 EPtot = -10253.6929 BOND = 22.6050 ANGLE = 69.7999 DIHED = 71.6118 1-4 NB = 35.2120 1-4 EEL = 535.2794 VDWAALS = 1393.4251 - EELEC = -12381.9867 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12381.9867 EHBOND = 0.0000 RESTRAINT = 0.3607 + EAMBER (non-restraint) = -10254.0536 Ewald error estimate: 0.1486E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.361 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.21 PRESS = 0.0 - Etot = -8317.8370 EKtot = 1904.9113 EPtot = -10222.7484 + Etot = -8317.4810 EKtot = 1904.9113 EPtot = -10222.3923 BOND = 27.3796 ANGLE = 66.5759 DIHED = 73.7294 1-4 NB = 32.0777 1-4 EEL = 535.9551 VDWAALS = 1380.9605 - EELEC = -12339.4267 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12339.4267 EHBOND = 0.0000 RESTRAINT = 0.3560 + EAMBER (non-restraint) = -10222.7484 Ewald error estimate: 0.1398E-03 ------------------------------------------------------------------------------ @@ -343,10 +386,11 @@ NGLY NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.48 PRESS = 0.0 - Etot = 6.0638 EKtot = 21.9953 EPtot = 23.0918 + Etot = 6.0749 EKtot = 21.9953 EPtot = 23.0951 BOND = 4.8775 ANGLE = 3.6365 DIHED = 1.2432 1-4 NB = 2.5153 1-4 EEL = 3.4586 VDWAALS = 38.2904 - EELEC = 40.2647 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 40.2647 EHBOND = 0.0000 RESTRAINT = 0.0237 + EAMBER (non-restraint) = 23.0714 Ewald error estimate: 0.1626E-03 ------------------------------------------------------------------------------ @@ -358,72 +402,72 @@ NGLY | | Routine Sec % | ------------------------------ -| DataDistrib 0.03 7.05 -| Nonbond 0.35 80.40 -| Bond 0.00 0.00 -| Angle 0.00 0.34 -| Dihedral 0.00 0.52 -| Shake 0.00 0.86 -| RunMD 0.04 10.03 -| Other 0.00 0.80 +| DataDistrib 0.01 3.26 +| Nonbond 0.20 80.36 +| Bond 0.00 0.10 +| Angle 0.00 0.30 +| Dihedral 0.00 0.49 +| Shake 0.00 1.18 +| RunMD 0.04 14.12 +| Other 0.00 0.20 | ------------------------------ -| Total 0.44 +| Total 0.25 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.23 -| Build List 0.03 7.97 +| Set Up Cit 0.00 0.20 +| Build List 0.02 7.90 | --------------------------------- -| Total 0.04 8.19 +| Total 0.02 8.09 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.21 48.48 -| Exclude Masked 0.00 0.80 -| Other 0.00 0.92 +| NonBonded Calc 0.12 45.71 +| Exclude Masked 0.00 0.79 +| Other 0.00 1.28 | --------------------------------- -| Total 0.22 50.20 +| Total 0.12 47.78 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.01 1.72 -| Grid Charges 0.01 1.72 -| Scalar Sum 0.02 3.67 -| Gradient Sum 0.01 2.87 -| FFT 0.05 11.92 +| 1D bspline 0.01 2.27 +| Grid Charges 0.00 1.38 +| Scalar Sum 0.01 3.26 +| Gradient Sum 0.01 3.75 +| FFT 0.03 13.82 | --------------------------------- -| Total 0.10 21.89 +| Total 0.06 24.48 | PME Load Balancing CPU Time, Average for All Tasks: | | Routine Sec % | ------------------------------------ | Atom Reassign 0.00 0.00 -| Image Reassign 0.00 0.11 +| Image Reassign 0.00 0.00 | FFT Reassign 0.00 0.00 | ------------------------------------ -| Total 0.00 0.11 +| Total 0.00 0.00 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 0.38 Per Step(ms) = 8.54 -| ns/day = 20.24 seconds/ns = 4268.81 +| Elapsed(s) = 0.22 Per Step(ms) = 4.92 +| ns/day = 35.15 seconds/ns = 2458.09 | | Average timings for all steps: -| Elapsed(s) = 0.47 Per Step(ms) = 9.35 -| ns/day = 18.48 seconds/ns = 4674.81 +| Elapsed(s) = 0.25 Per Step(ms) = 5.10 +| ns/day = 33.89 seconds/ns = 2549.72 | ----------------------------------------------------- | Master Setup CPU time: 0.08 seconds -| Master NonSetup CPU time: 0.43 seconds -| Master Total CPU time: 0.51 seconds 0.00 hours +| Master NonSetup CPU time: 0.25 seconds +| Master Total CPU time: 0.33 seconds 0.00 hours | Master Setup wall time: 0 seconds | Master NonSetup wall time: 0 seconds diff --git test/nfe/pmd/save.sander/mdout test/nfe/pmd/save.sander/mdout index a33404a920..1f2e9325a8 100644 --- test/nfe/pmd/save.sander/mdout +++ test/nfe/pmd/save.sander/mdout @@ -1,14 +1,15 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 01/18/2017 at 09:32:12 +| Run on 09/05/2018 at 13:00:54 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/pmd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/pmd +| Hostname: gaia.physics.ncsu.edu + [-O]verwriting output File Assignments: | MDIN: mdin @@ -169,7 +170,7 @@ NGLY NFE : output_file = pmd.txt NFE : output_freq = 1 (0.0020 ps) NFE : - NFE : CV #1 << anchor : position = 0.000000,6.000000, 6.000000, 12.000000 + NFE : CV #1 << anchor : position = 0.000000, 6.000000, 6.000000, 12.000000 NFE : strength = 10.000000, 10.000000 >> NFE : type = 'MULTI_RMSD' NFE : <> group <> #1: @@ -228,103 +229,144 @@ NGLY | TOTAL SIZE OF NONBOND LIST = 650668 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.5188 EKtot = 1914.1465 EPtot = -10235.6653 + Etot = -8321.2195 EKtot = 1914.1465 EPtot = -10235.3660 BOND = 19.0663 ANGLE = 63.5971 DIHED = 72.6948 1-4 NB = 31.9335 1-4 EEL = 541.0087 VDWAALS = 1297.2725 - EELEC = -12261.2382 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2382 EHBOND = 0.0000 RESTRAINT = 0.2993 + EAMBER (non-restraint) = -10235.6653 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.299 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.14 PRESS = 0.0 - Etot = -8329.4106 EKtot = 1917.1217 EPtot = -10246.5323 + Etot = -8329.0697 EKtot = 1917.1217 EPtot = -10246.1914 BOND = 25.2397 ANGLE = 68.0814 DIHED = 73.1111 1-4 NB = 34.0214 1-4 EEL = 541.6821 VDWAALS = 1326.2580 - EELEC = -12314.9261 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9261 EHBOND = 0.0000 RESTRAINT = 0.3410 + EAMBER (non-restraint) = -10246.5323 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.341 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.20 PRESS = 0.0 - Etot = -8320.1632 EKtot = 1879.5929 EPtot = -10199.7561 + Etot = -8319.8177 EKtot = 1879.5929 EPtot = -10199.4106 BOND = 25.7019 ANGLE = 67.6557 DIHED = 76.3006 1-4 NB = 31.5105 1-4 EEL = 535.1205 VDWAALS = 1359.5128 - EELEC = -12295.5581 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12295.5581 EHBOND = 0.0000 RESTRAINT = 0.3455 + EAMBER (non-restraint) = -10199.7561 Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.345 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.16 PRESS = 0.0 - Etot = -8312.0451 EKtot = 1891.9709 EPtot = -10204.0160 + Etot = -8311.7006 EKtot = 1891.9709 EPtot = -10203.6715 BOND = 32.7904 ANGLE = 68.1904 DIHED = 72.9052 1-4 NB = 28.4265 1-4 EEL = 536.5292 VDWAALS = 1387.0497 - EELEC = -12329.9074 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12329.9074 EHBOND = 0.0000 RESTRAINT = 0.3445 + EAMBER (non-restraint) = -10204.0160 Ewald error estimate: 0.2698E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.345 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.79 PRESS = 0.0 - Etot = -8313.6990 EKtot = 1908.6139 EPtot = -10222.3129 + Etot = -8313.3394 EKtot = 1908.6139 EPtot = -10221.9533 BOND = 35.3907 ANGLE = 70.7942 DIHED = 73.4732 1-4 NB = 28.9331 1-4 EEL = 539.0462 VDWAALS = 1406.8022 - EELEC = -12376.7525 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12376.7525 EHBOND = 0.0000 RESTRAINT = 0.3596 + EAMBER (non-restraint) = -10222.3129 Ewald error estimate: 0.3145E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.360 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.88 PRESS = 0.0 - Etot = -8308.2644 EKtot = 1947.0813 EPtot = -10255.3457 + Etot = -8307.8807 EKtot = 1947.0813 EPtot = -10254.9620 BOND = 32.7694 ANGLE = 64.3710 DIHED = 74.4239 1-4 NB = 30.2552 1-4 EEL = 534.7202 VDWAALS = 1408.1058 - EELEC = -12399.9912 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12399.9912 EHBOND = 0.0000 RESTRAINT = 0.3837 + EAMBER (non-restraint) = -10255.3457 Ewald error estimate: 0.7653E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.384 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 295.99 PRESS = 0.0 - Etot = -8312.4601 EKtot = 1871.9225 EPtot = -10184.3826 + Etot = -8312.0834 EKtot = 1871.9225 EPtot = -10184.0059 BOND = 23.7048 ANGLE = 70.7963 DIHED = 73.5110 1-4 NB = 30.2050 1-4 EEL = 531.3801 VDWAALS = 1412.1586 - EELEC = -12326.1383 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12326.1383 EHBOND = 0.0000 RESTRAINT = 0.3767 + EAMBER (non-restraint) = -10184.3826 Ewald error estimate: 0.7180E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.377 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.06 PRESS = 0.0 - Etot = -8316.4360 EKtot = 1897.6776 EPtot = -10214.1136 + Etot = -8316.0627 EKtot = 1897.6776 EPtot = -10213.7403 BOND = 27.5475 ANGLE = 63.4108 DIHED = 74.6817 1-4 NB = 34.6278 1-4 EEL = 531.2967 VDWAALS = 1411.0707 - EELEC = -12356.7488 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12356.7488 EHBOND = 0.0000 RESTRAINT = 0.3733 + EAMBER (non-restraint) = -10214.1136 Ewald error estimate: 0.2753E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.373 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 298.93 PRESS = 0.0 - Etot = -8320.8144 EKtot = 1890.4910 EPtot = -10211.3054 + Etot = -8320.4383 EKtot = 1890.4910 EPtot = -10210.9293 BOND = 28.9803 ANGLE = 59.0628 DIHED = 74.5811 1-4 NB = 35.6516 1-4 EEL = 533.4882 VDWAALS = 1407.9501 - EELEC = -12351.0195 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12351.0195 EHBOND = 0.0000 RESTRAINT = 0.3761 + EAMBER (non-restraint) = -10211.3054 Ewald error estimate: 0.1509E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.376 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.25 PRESS = 0.0 - Etot = -8323.5586 EKtot = 1930.4950 EPtot = -10254.0536 + Etot = -8323.1979 EKtot = 1930.4950 EPtot = -10253.6929 BOND = 22.6050 ANGLE = 69.7999 DIHED = 71.6118 1-4 NB = 35.2120 1-4 EEL = 535.2794 VDWAALS = 1393.4251 - EELEC = -12381.9867 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12381.9867 EHBOND = 0.0000 RESTRAINT = 0.3607 + EAMBER (non-restraint) = -10254.0536 Ewald error estimate: 0.1486E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.361 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 50 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 300.63 PRESS = 0.0 - Etot = -8317.4592 EKtot = 1901.2500 EPtot = -10218.7093 + Etot = -8317.1068 EKtot = 1901.2500 EPtot = -10218.3568 BOND = 28.8978 ANGLE = 67.5155 DIHED = 73.8177 1-4 NB = 32.0141 1-4 EEL = 536.1909 VDWAALS = 1376.2164 - EELEC = -12333.3616 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12333.3616 EHBOND = 0.0000 RESTRAINT = 0.3524 + EAMBER (non-restraint) = -10218.7093 Ewald error estimate: 0.1691E-03 ------------------------------------------------------------------------------ @@ -333,10 +375,11 @@ NGLY NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.25 PRESS = 0.0 - Etot = 6.8792 EKtot = 20.5512 EPtot = 20.6018 + Etot = 6.8992 EKtot = 20.5512 EPtot = 20.6058 BOND = 4.5996 ANGLE = 4.1057 DIHED = 1.9527 1-4 NB = 2.4116 1-4 EEL = 3.6760 VDWAALS = 43.5645 - EELEC = 42.1859 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 42.1859 EHBOND = 0.0000 RESTRAINT = 0.0293 + EAMBER (non-restraint) = 20.5765 Ewald error estimate: 0.1609E-03 ------------------------------------------------------------------------------ @@ -346,42 +389,41 @@ NGLY -------------------------------------------------------------------------------- |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> -| Read coords time 0.00 ( 0.29% of Total) +| Read coords time 0.00 ( 0.30% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.08 (72.71% of List ) -| Other 0.03 (27.29% of List ) -| List time 0.10 (13.91% of Nonbo) -| Short_ene time 0.46 (97.33% of Direc) -| Other 0.01 ( 2.67% of Direc) -| Direct Ewald time 0.48 (73.78% of Ewald) -| Adjust Ewald time 0.00 ( 0.58% of Ewald) +| Build the list 0.04 (75.37% of List ) +| Other 0.01 (24.63% of List ) +| List time 0.06 (13.41% of Nonbo) +| Short_ene time 0.26 (97.29% of Direc) +| Other 0.01 ( 2.71% of Direc) +| Direct Ewald time 0.27 (74.10% of Ewald) +| Adjust Ewald time 0.00 ( 0.49% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.01 ( 6.84% of Recip) -| Fill charge grid 0.01 ( 6.91% of Recip) -| Scalar sum 0.06 (37.46% of Recip) -| Grad sum 0.02 (14.93% of Recip) -| FFT back comm time 0.01 (13.08% of FFT t) -| Other 0.04 (86.92% of FFT t) -| FFT time 0.05 (33.37% of Recip) -| Other 0.00 ( 0.48% of Recip) -| Recip Ewald time 0.15 (23.08% of Ewald) +| Fill Bspline coeffs 0.01 ( 7.34% of Recip) +| Fill charge grid 0.01 ( 7.31% of Recip) +| Scalar sum 0.03 (33.51% of Recip) +| Grad sum 0.01 (15.95% of Recip) +| FFT back comm time 0.00 (11.98% of FFT t) +| Other 0.03 (88.02% of FFT t) +| FFT time 0.03 (35.52% of Recip) +| Other 0.00 ( 0.38% of Recip) +| Recip Ewald time 0.08 (22.83% of Ewald) | Force Adjust 0.01 ( 2.23% of Ewald) -| Virial junk 0.00 ( 0.24% of Ewald) +| Virial junk 0.00 ( 0.25% of Ewald) | Other 0.00 ( 0.08% of Ewald) -| Ewald time 0.64 (86.08% of Nonbo) -| Other 0.00 ( 0.01% of Nonbo) -| Nonbond force 0.75 (98.18% of Force) +| Ewald time 0.36 (86.58% of Nonbo) +| Nonbond force 0.42 (98.43% of Force) | Bond/Angle/Dihedral 0.00 ( 0.44% of Force) -| FRC Collect time 0.00 ( 0.40% of Force) -| Other 0.01 ( 0.97% of Force) -| Force time 0.76 (89.67% of Runmd) -| Shake time 0.00 ( 0.56% of Runmd) -| Verlet update time 0.08 ( 9.16% of Runmd) -| CRD distribute time 0.00 ( 0.18% of Runmd) -| Other 0.00 ( 0.42% of Runmd) -| Runmd Time 0.85 (89.66% of Total) -| Other 0.10 (10.04% of Total) -| Total time 0.95 (98.16% of ALL ) +| FRC Collect time 0.00 ( 0.39% of Force) +| Other 0.00 ( 0.74% of Force) +| Force time 0.42 (88.59% of Runmd) +| Shake time 0.00 ( 0.45% of Runmd) +| Verlet update time 0.05 ( 9.85% of Runmd) +| CRD distribute time 0.00 ( 0.17% of Runmd) +| Other 0.00 ( 0.94% of Runmd) +| Runmd Time 0.48 (91.49% of Total) +| Other 0.04 ( 8.19% of Total) +| Total time 0.52 (99.81% of ALL ) | Number of list builds : 5 @@ -391,11 +433,11 @@ NGLY | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 0.85 Per Step(ms) = 17.04 -| ns/day = 10.14 seconds/ns = 8519.53 +| Elapsed(s) = 0.48 Per Step(ms) = 9.55 +| ns/day = 18.09 seconds/ns = 4776.64 | ----------------------------------------------------- -| Job began at 09:32:12.424 on 01/18/2017 -| Setup done at 09:32:12.542 on 01/18/2017 -| Run done at 09:32:13.394 on 01/18/2017 +| Job began at 13:00:54.297 on 09/05/2018 +| Setup done at 13:00:54.342 on 09/05/2018 +| Run done at 13:00:54.820 on 09/05/2018 | wallclock() was called 2783 times diff --git test/nfe/pmd/save.sander/pmd.txt test/nfe/pmd/save.sander/pmd.txt index dbf38fa1af..0ceed83afe 100644 --- test/nfe/pmd/save.sander/pmd.txt +++ test/nfe/pmd/save.sander/pmd.txt @@ -1,5 +1,5 @@ # = NFE%PMD ================================================================== -# << anchor(1) : position = 0.000000,6.000000, 6.000000, 12.000000 +# << anchor(1) : position = 0.000000, 6.000000, 6.000000, 12.000000 # strength = 10.000000, 10.000000 >> # ----------------------------------------------------------------------------- # MD time (ps), CV(1:1) diff --git test/nfe/premd/inpcrd.1 test/nfe/premd/inpcrd.1 index 73d7aa7338..0289652b43 100644 --- test/nfe/premd/inpcrd.1 +++ test/nfe/premd/inpcrd.1 @@ -1,5 +1,5 @@ NGLY - 3143 0.0000000E+00 0.3200000E+03 + 3143 0.0000000E+00 -5.9099758 16.7611687 9.6964744 -6.6876601 16.2962589 10.1427587 -5.6077881 16.2415689 8.8848103 -6.0729168 17.6175205 9.1863747 -4.7182170 16.6491281 10.4618789 -4.3645304 15.6209508 10.3853468 diff --git test/nfe/premd/inpcrd.2 test/nfe/premd/inpcrd.2 index 2ee93e4c83..88fc07ea29 100644 --- test/nfe/premd/inpcrd.2 +++ test/nfe/premd/inpcrd.2 @@ -1,5 +1,5 @@ NGLY - 3143 0.0000000E+00 0.3000000E+03 + 3143 0.0000000E+00 -6.3647119 7.2118689 4.2338885 -5.7620774 6.8676748 3.5000899 -5.6693358 7.4541444 4.9251589 -6.7424291 8.0670351 3.8516314 -7.3862977 6.2756135 4.6925230 -8.1140353 6.0876054 3.9031273 diff --git test/nfe/premd/inpcrd.3 test/nfe/premd/inpcrd.3 index 3370f6a0c0..d5c10b2b42 100644 --- test/nfe/premd/inpcrd.3 +++ test/nfe/premd/inpcrd.3 @@ -1,5 +1,5 @@ NGLY - 3143 0.0000000E+00 0.3300000E+03 + 3143 0.0000000E+00 -4.8563545 15.0635235 25.8712062 -4.5271096 16.0127985 25.7683623 -3.9707341 14.5801650 25.9174805 -5.4031234 14.8420339 26.6910147 -5.6050883 14.7641396 24.6600085 -6.1061885 13.7996469 24.7421811 diff --git test/nfe/premd/inpcrd.4 test/nfe/premd/inpcrd.4 index fdc15b3027..4800fa9afd 100644 --- test/nfe/premd/inpcrd.4 +++ test/nfe/premd/inpcrd.4 @@ -1,5 +1,5 @@ NGLY - 3143 0.0000000E+00 0.3100000E+03 + 3143 0.0000000E+00 1.8785779 25.3661554 7.7188732 1.7220016 25.2727944 8.7122864 2.5527229 24.6529067 7.4803257 1.0934459 25.1537287 7.1200889 2.4401376 26.6274332 7.3917997 2.4565905 26.7008661 6.3044000 diff --git test/nfe/premd/mdin.1 test/nfe/premd/mdin.1 index 779d8cd85b..fd6dede810 100644 --- test/nfe/premd/mdin.1 +++ test/nfe/premd/mdin.1 @@ -4,7 +4,7 @@ ntb = 1, ntp = 0, temp0 = 300.0, ntt = 1, gamma_ln = 0.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, numexchg = 10, infe = 1, / diff --git test/nfe/premd/mdin.2 test/nfe/premd/mdin.2 index 8c3c2c48e8..5f85b6e5db 100644 --- test/nfe/premd/mdin.2 +++ test/nfe/premd/mdin.2 @@ -4,7 +4,7 @@ ntb = 1, ntp = 0, temp0 = 310.0, ntt = 1, gamma_ln = 0.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, numexchg = 10, infe = 1, / diff --git test/nfe/premd/mdin.3 test/nfe/premd/mdin.3 index 96880e10c4..c9c7c111e1 100644 --- test/nfe/premd/mdin.3 +++ test/nfe/premd/mdin.3 @@ -4,7 +4,7 @@ ntb = 1, ntp = 0, temp0 = 320.0, ntt = 1, gamma_ln = 0.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, numexchg = 10, infe = 1, / diff --git test/nfe/premd/mdin.4 test/nfe/premd/mdin.4 index 8b13f80dae..9740a852a9 100644 --- test/nfe/premd/mdin.4 +++ test/nfe/premd/mdin.4 @@ -4,7 +4,7 @@ ntb = 1, ntp = 0, temp0 = 330.0, ntt = 1, gamma_ln = 0.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, numexchg = 10, infe = 1, / diff --git test/nfe/premd/run-pmemd.sh test/nfe/premd/run-pmemd.sh new file mode 100755 index 0000000000..c9f7dda324 --- /dev/null +++ test/nfe/premd/run-pmemd.sh @@ -0,0 +1,49 @@ +#!/bin/sh +#TEST-PROGRAM sander +#TEST-DESCRIP TO_BE_DEtermined +#TEST-PURPOSE regression, basic +#TEST-STATE undocumented + +. ../common.sh + +set_SANDER pmemd.MPI +set_SANDER_CMD 4 + +JUNK="mdout.? restrt.? pmd.?.txt groups prmtop sander.out *.log *.type logfile.*" + +# +# remove the junk +# + +/bin/rm -rf ${JUNK} junk.* + +# +# prepare files +# + +cp -p ../prmtop ../groups . + +# +# run SANDER +# + +${SANDER_CMD} -ng 4 -rem 3 -groupfile groups > sander.out 2>&1 + +../../dacdif save/rem.log rem.log + +for i in 1 2 3 4; do + ../../dacdif -t 1 save/pmd.$i.txt.pmemd pmd.$i.txt + ../../dacdif -t 1 save/mdout.$i.pmemd mdout.$i +done + +# +# preserve the junk on failure +# + +save_junk_on_failure ${JUNK} + +# +# remove the junk +# + +/bin/rm -f ${JUNK} profile_mpi diff --git test/nfe/premd/run-sander.sh test/nfe/premd/run-sander.sh index 86b28dc30b..106569b8bf 100755 --- test/nfe/premd/run-sander.sh +++ test/nfe/premd/run-sander.sh @@ -27,12 +27,10 @@ cp -p ../prmtop ../groups . # run SANDER # -${SANDER_CMD} -ng 4 -rem 1 -groupfile groups > sander.out 2>&1 +${SANDER_CMD} -ng 4 -rem 3 -groupfile groups > sander.out 2>&1 ../../dacdif save/rem.log rem.log -../../dacdif save/nfe-pmd.log nfe-pmd.log - for i in 1 2 3 4; do ../../dacdif -t 1 save/pmd.$i.txt pmd.$i.txt ../../dacdif -t 1 save/mdout.$i mdout.$i diff --git test/nfe/premd/save/mdout.1 test/nfe/premd/save/mdout.1 index 964c099fb1..0a61372456 100644 --- test/nfe/premd/save/mdout.1 +++ test/nfe/premd/save/mdout.1 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/14/2016 at 17:59:34 +| Run on 09/21/2018 at 19:24:35 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/premd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/premd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -45,9 +45,9 @@ File Assignments: ntb = 1, ntp = 0, temp0 = 300.0, ntt = 1, gamma_ln = 0.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, - numexchg = 10, infe = 1, + numexchg = 10, infe = 1, / &pmd @@ -83,8 +83,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -106,7 +106,7 @@ General flags: imin = 0, nmropt = 0 Replica exchange - numexchg= 10, rem= 1 + numexchg= 10, rem= 3 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 @@ -157,18 +157,35 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + NFE : + NFE : output_file = pmd.1.txt + NFE : output_freq = 1 (0.0020 ps) + NFE : + NFE : CV #1 << anchor : position = 0.000000, 5.000000, 5.000000, 10.000000 + NFE : strength = 1.000000, 1.000000 >> + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + | # of SOLUTE degrees of freedom (RNDFP): 6365. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 6362. NUM_NOSHAKE = 0 CORRECTED RNDFP = 6362. @@ -180,158 +197,202 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 650835 +| Local SIZE OF NONBOND LIST = 329344 | TOTAL SIZE OF NONBOND LIST = 650835 - NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 308.46 PRESS = 0.0 - Etot = -8191.9335 EKtot = 1949.8269 EPtot = -10141.7604 - BOND = 21.3592 ANGLE = 62.9920 DIHED = 75.1460 - 1-4 NB = 33.2954 1-4 EEL = 538.2938 VDWAALS = 1413.8330 - EELEC = -12286.6797 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1123E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 1 + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 282.73 PRESS = 0.0 + Etot = -8478.8325 EKtot = 1787.1870 EPtot = -10266.0195 + BOND = 28.8372 ANGLE = 52.2592 DIHED = 71.7541 + 1-4 NB = 28.6467 1-4 EEL = 540.2183 VDWAALS = 1437.1983 + EELEC = -12425.7867 EHBOND = 0.0000 RESTRAINT = 0.8535 + EAMBER (non-restraint) = -10266.8730 + Ewald error estimate: 0.4142E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 1 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 308.74 PRESS = 0.0 - Etot = -8190.5386 EKtot = 1951.6161 EPtot = -10142.1547 - BOND = 30.8569 ANGLE = 71.7459 DIHED = 77.9522 - 1-4 NB = 33.2538 1-4 EEL = 533.8082 VDWAALS = 1411.1891 - EELEC = -12300.9606 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.7252E-04 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 2 + NFE restraints: SMD : 0.000 PMD : 0.854 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 283.14 PRESS = 0.0 + Etot = -8506.2197 EKtot = 1789.7840 EPtot = -10296.0037 + BOND = 23.2600 ANGLE = 77.1238 DIHED = 74.6823 + 1-4 NB = 31.2022 1-4 EEL = 514.4454 VDWAALS = 1406.5703 + EELEC = -12426.0523 EHBOND = 0.0000 RESTRAINT = 2.7645 + EAMBER (non-restraint) = -10298.7682 + Ewald error estimate: 0.4337E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 2 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 313.60 PRESS = 0.0 - Etot = -8190.3447 EKtot = 1982.3426 EPtot = -10172.6874 - BOND = 22.9563 ANGLE = 72.3867 DIHED = 72.6983 - 1-4 NB = 32.4638 1-4 EEL = 540.9330 VDWAALS = 1413.2107 - EELEC = -12327.3363 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.9479E-04 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 3 + NFE restraints: SMD : 0.000 PMD : 2.765 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 280.24 PRESS = 0.0 + Etot = -8505.1284 EKtot = 1771.4852 EPtot = -10276.6136 + BOND = 26.3807 ANGLE = 67.1346 DIHED = 76.7580 + 1-4 NB = 31.9009 1-4 EEL = 519.5149 VDWAALS = 1410.6846 + EELEC = -12411.7329 EHBOND = 0.0000 RESTRAINT = 2.7455 + EAMBER (non-restraint) = -10279.3591 + Ewald error estimate: 0.4092E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 3 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 308.93 PRESS = 0.0 - Etot = -8189.0965 EKtot = 1952.8242 EPtot = -10141.9208 - BOND = 30.8886 ANGLE = 74.2759 DIHED = 75.6979 - 1-4 NB = 35.5064 1-4 EEL = 541.9156 VDWAALS = 1408.3257 - EELEC = -12308.5308 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1637E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 4 + NFE restraints: SMD : 0.000 PMD : 2.745 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 285.52 PRESS = 0.0 + Etot = -8504.4859 EKtot = 1804.8271 EPtot = -10309.3129 + BOND = 25.8049 ANGLE = 69.7632 DIHED = 71.1631 + 1-4 NB = 29.8081 1-4 EEL = 524.5095 VDWAALS = 1405.2455 + EELEC = -12438.3290 EHBOND = 0.0000 RESTRAINT = 2.7217 + EAMBER (non-restraint) = -10312.0347 + Ewald error estimate: 0.2360E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 4 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 306.64 PRESS = 0.0 - Etot = -8188.2702 EKtot = 1938.3362 EPtot = -10126.6064 - BOND = 31.0911 ANGLE = 60.9673 DIHED = 79.1863 - 1-4 NB = 32.6080 1-4 EEL = 541.2454 VDWAALS = 1414.0467 - EELEC = -12285.7512 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.9438E-04 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 5 + NFE restraints: SMD : 0.000 PMD : 2.722 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 283.36 PRESS = 0.0 + Etot = -8503.4675 EKtot = 1791.1976 EPtot = -10294.6651 + BOND = 23.5705 ANGLE = 66.9791 DIHED = 72.4567 + 1-4 NB = 33.0260 1-4 EEL = 528.4085 VDWAALS = 1412.2146 + EELEC = -12434.0060 EHBOND = 0.0000 RESTRAINT = 2.6856 + EAMBER (non-restraint) = -10297.3506 + Ewald error estimate: 0.9501E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 5 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 302.08 PRESS = 0.0 - Etot = -8187.5197 EKtot = 1909.5282 EPtot = -10097.0479 - BOND = 31.8230 ANGLE = 61.3542 DIHED = 82.7680 - 1-4 NB = 34.9606 1-4 EEL = 538.1481 VDWAALS = 1436.3696 - EELEC = -12282.4712 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.6597E-04 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 6 + NFE restraints: SMD : 0.000 PMD : 2.686 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 281.46 PRESS = 0.0 + Etot = -8470.3960 EKtot = 1779.1542 EPtot = -10249.5502 + BOND = 25.7761 ANGLE = 55.8022 DIHED = 75.3272 + 1-4 NB = 34.0068 1-4 EEL = 534.2188 VDWAALS = 1442.9203 + EELEC = -12418.4273 EHBOND = 0.0000 RESTRAINT = 0.8258 + EAMBER (non-restraint) = -10250.3760 + Ewald error estimate: 0.7505E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 6 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 299.23 PRESS = 0.0 - Etot = -8186.6808 EKtot = 1891.5141 EPtot = -10078.1949 - BOND = 30.3744 ANGLE = 61.5217 DIHED = 76.8279 - 1-4 NB = 36.0306 1-4 EEL = 541.7661 VDWAALS = 1434.3486 - EELEC = -12259.0642 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3189E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 7 + NFE restraints: SMD : 0.000 PMD : 0.826 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 287.94 PRESS = 0.0 + Etot = -8470.1317 EKtot = 1820.1163 EPtot = -10290.2480 + BOND = 21.0300 ANGLE = 60.8428 DIHED = 78.6979 + 1-4 NB = 33.2464 1-4 EEL = 540.2732 VDWAALS = 1435.6969 + EELEC = -12460.8499 EHBOND = 0.0000 RESTRAINT = 0.8147 + EAMBER (non-restraint) = -10291.0627 + Ewald error estimate: 0.6979E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 7 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 295.30 PRESS = 0.0 - Etot = -8185.2091 EKtot = 1866.6767 EPtot = -10051.8858 - BOND = 22.4283 ANGLE = 69.7166 DIHED = 77.4626 - 1-4 NB = 39.1631 1-4 EEL = 536.5084 VDWAALS = 1386.3840 - EELEC = -12183.5489 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1409E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 8 + NFE restraints: SMD : 0.000 PMD : 0.815 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 282.37 PRESS = 0.0 + Etot = -8468.4104 EKtot = 1784.9530 EPtot = -10253.3634 + BOND = 29.4089 ANGLE = 51.1135 DIHED = 79.9810 + 1-4 NB = 32.3287 1-4 EEL = 541.0447 VDWAALS = 1433.8589 + EELEC = -12421.9006 EHBOND = 0.0000 RESTRAINT = 0.8015 + EAMBER (non-restraint) = -10254.1649 + Ewald error estimate: 0.2309E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 8 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 298.26 PRESS = 0.0 - Etot = -8183.7527 EKtot = 1885.3624 EPtot = -10069.1151 - BOND = 25.4508 ANGLE = 74.5050 DIHED = 76.6153 - 1-4 NB = 38.7566 1-4 EEL = 537.4735 VDWAALS = 1326.8868 - EELEC = -12148.8032 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2707E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 9 + NFE restraints: SMD : 0.000 PMD : 0.802 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 286.43 PRESS = 0.0 + Etot = -8468.0040 EKtot = 1810.5811 EPtot = -10278.5852 + BOND = 27.3024 ANGLE = 54.3433 DIHED = 76.9280 + 1-4 NB = 33.0109 1-4 EEL = 543.0536 VDWAALS = 1452.5261 + EELEC = -12466.5490 EHBOND = 0.0000 RESTRAINT = 0.7996 + EAMBER (non-restraint) = -10279.3848 + Ewald error estimate: 0.1823E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 9 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 307.19 PRESS = 0.0 - Etot = -8183.3489 EKtot = 1941.8248 EPtot = -10125.1738 - BOND = 24.4369 ANGLE = 66.1522 DIHED = 71.8016 - 1-4 NB = 34.6506 1-4 EEL = 539.4673 VDWAALS = 1300.8131 - EELEC = -12162.4954 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3237E-03 - TEMP0 = 320.0000 REPNUM = 1 EXCHANGE# = 10 + NFE restraints: SMD : 0.000 PMD : 0.800 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 278.83 PRESS = 0.0 + Etot = -8495.0926 EKtot = 1762.5288 EPtot = -10257.6214 + BOND = 25.2470 ANGLE = 68.4638 DIHED = 72.4801 + 1-4 NB = 32.6143 1-4 EEL = 519.9378 VDWAALS = 1396.9670 + EELEC = -12375.8681 EHBOND = 0.0000 RESTRAINT = 2.5366 + EAMBER (non-restraint) = -10260.1580 + Ewald error estimate: 0.7212E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 10 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 2.537 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.30% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.00 ( 0.14% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.30 (90.98% of List ) -| Other 0.03 ( 9.02% of List ) -| List time 0.33 ( 9.77% of Nonbo) -| Short_ene time 2.28 (99.09% of Direc) -| Other 0.02 ( 0.91% of Direc) -| Direct Ewald time 2.30 (76.67% of Ewald) -| Adjust Ewald time 0.02 ( 0.63% of Ewald) -| Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.03 ( 4.29% of Recip) -| Fill charge grid 0.05 ( 7.53% of Recip) -| Scalar sum 0.28 (40.73% of Recip) -| Grad sum 0.11 (16.32% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.21 (100.0% of FFT t) -| FFT time 0.21 (31.11% of Recip) -| Other 0.00 ( 0.03% of Recip) -| Recip Ewald time 0.68 (22.56% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.05% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 3.01 (90.22% of Nonbo) -| Nonbond force 3.33 (98.91% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.48% of Force) -| Other 0.02 ( 0.61% of Force) -| Force time 3.37 (94.52% of Runmd) -| Shake time 0.02 ( 0.47% of Runmd) -| Verlet update time 0.01 ( 0.38% of Runmd) -| Other 0.16 ( 4.62% of Runmd) -| Runmd Time 3.56 (98.33% of Total) -| Other 0.05 ( 1.36% of Total) -| Total time 3.62 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Build the list 0.43 (95.96% of List ) +| Other 0.02 ( 4.04% of List ) +| List time 0.45 (22.06% of Nonbo) +| Short_ene time 0.96 (97.92% of Direc) +| Other 0.02 ( 2.08% of Direc) +| Direct Ewald time 0.98 (61.47% of Ewald) +| Adjust Ewald time 0.01 ( 0.43% of Ewald) +| Fill Bspline coeffs 0.02 ( 6.05% of Recip) +| Fill charge grid 0.03 ( 6.13% of Recip) +| Scalar sum 0.10 (24.43% of Recip) +| Grad sum 0.06 (13.72% of Recip) +| FFT back comm time 0.01 ( 7.51% of FFT t) +| Other 0.16 (92.49% of FFT t) +| FFT time 0.17 (42.53% of Recip) +| Other 0.03 ( 7.14% of Recip) +| Recip Ewald time 0.41 (25.72% of Ewald) +| Force Adjust 0.19 (12.18% of Ewald) +| Virial junk 0.00 ( 0.13% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.59 (77.94% of Nonbo) +| Nonbond force 2.04 (99.33% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.35% of Force) +| FRC Collect time 0.00 ( 0.13% of Force) +| Other 0.00 ( 0.19% of Force) +| Force time 2.05 (95.58% of Runmd) +| Shake time 0.00 ( 0.22% of Runmd) +| Verlet update time 0.01 ( 0.31% of Runmd) +| CRD distribute time 0.00 ( 0.04% of Runmd) +| Other 0.08 ( 3.86% of Runmd) +| Runmd Time 2.15 (97.37% of Total) +| Other 0.05 ( 2.48% of Total) +| Total time 2.21 (100.0% of ALL ) + +| Number of list builds : 17 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 3.56 Per Step(ms) = 71.29 -| ns/day = 2.42 seconds/ns = 35642.97 +| Elapsed(s) = 2.15 Per Step(ms) = 42.98 +| ns/day = 4.02 seconds/ns = 21489.77 | ----------------------------------------------------- -| Job began at 17:59:34.530 on 06/14/2016 -| Setup done at 17:59:34.592 on 06/14/2016 -| Run done at 17:59:38.156 on 06/14/2016 -| wallclock() was called 3211 times +| Job began at 19:24:35.570 on 09/21/2018 +| Setup done at 19:24:35.629 on 09/21/2018 +| Run done at 19:24:37.778 on 09/21/2018 +| wallclock() was called 3775 times diff --git test/nfe/premd/save/mdout.1.pmemd test/nfe/premd/save/mdout.1.pmemd new file mode 100644 index 0000000000..bc404ae7d0 --- /dev/null +++ test/nfe/premd/save/mdout.1.pmemd @@ -0,0 +1,429 @@ + + ------------------------------------------------------- + Amber 18 PMEMD 2018 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 18 + +| Run on 09/21/2018 at 19:25:45 + +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/premd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output + +File Assignments: +| MDIN: mdin.1 +| MDOUT: mdout.1 +| INPCRD: inpcrd.1 +| PARM: prmtop +| RESTRT: restrt.1 +| REFC: refc +| MDVEL: mdvel.000 +| MDEN: mden.000 +| MDCRD: mdcrd.1 +| MDINFO: /dev/null +|LOGFILE: logfile.000 +| MDFRC: mdfrc.000 + + + Here is the input file: + + + &cntrl + igb = 0, ntx = 7, irest = 1, + ntb = 1, ntp = 0, temp0 = 300.0, + ntt = 1, gamma_ln = 0.0, + ntf = 2, ntc = 2, tol = 0.00001, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, + numexchg = 10, infe = 1, + / + + &pmd + output_file = 'pmd.1.txt' + output_freq = 1 + cv_file = 'cv.1' + / + + +| irandom = 1, using AMBER's internal random number generator (default). + + +| Conditional Compilation Defines Used: +| MPI +| PUBFFT +| BINTRAJ +| EMIL + +| Largest sphere to fit in unit cell has radius = 14.075 + +| New format PARM file being parsed. +| Version = 1.000 Date = 09/01/07 Time = 11:29:05 + +| Note: 1-4 EEL scale factors were NOT found in the topology file. +| Using default value of 1.2. + +| Note: 1-4 VDW scale factors were NOT found in the topology file. +| Using default value of 2.0. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 + NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 + NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 + NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 + NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 + IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 6 6 6 +| Direct force subcell size = 5.7460 5.7460 5.7460 + + BOX TYPE: TRUNCATED OCTAHEDRON + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + +NGLY + +General flags: + imin = 0, nmropt = 0 + +Replica exchange + numexchg= 10, rem= 3 + +Nature and format of input: + ntx = 7, irest = 1, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 5, ntrx = 1, ntwr = 50 + iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 2, ntb = 1, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 0 + +Molecular dynamics: + nstlim = 5, nscm = 1000, nrespa = 1 + t = 0.00000, dt = 0.00200, vlimit = 20.00000 + +Berendsen (weak-coupling) temperature regulation: + temp0 = 300.00000, tempi = 0.00000, tautp = 1.00000 + +SHAKE: + ntc = 2, jfastw = 0 + tol = 0.00001 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 5 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 1 + Box X = 34.476 Box Y = 34.476 Box Z = 34.476 + Alpha = 109.471 Beta = 109.471 Gamma = 109.471 + NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + +NGLY + begin time read from input coords = 0.000 ps + + + Number of triangulated 3-point waters found: 1001 + + Sum of charges from parm topology file = -0.00000001 + Forcing neutrality... + +| Dynamic Memory, Types Used: +| Reals 245734 +| Integers 212431 + +| Nonbonded Pairs Initial Allocation: 358302 + +| Running AMBER/MPI version on 2 MPI task + + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + --------------------------------------------------- + APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION + using 5000.0 points per unit in tabled values + TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff +| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 +| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 + --------------------------------------------------- +|--------------------------------------------------- +| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.47 +| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.89 +|--------------------------------------------------- + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + NFE : + NFE : output_file = pmd.1.txt + NFE : output_freq = 1 (0.0020 ps) + NFE : + NFE : CV #1 << anchor : position = 0.000000, 5.000000, 5.000000, 10.000000 + NFE : strength = 1.000000, 1.000000 >> + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + + + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 282.73 PRESS = 0.0 + Etot = -8478.8325 EKtot = 1787.1870 EPtot = -10266.0195 + BOND = 28.8372 ANGLE = 52.2592 DIHED = 71.7541 + 1-4 NB = 28.6467 1-4 EEL = 540.2183 VDWAALS = 1437.1983 + EELEC = -12425.7867 EHBOND = 0.0000 RESTRAINT = 0.8535 + EAMBER (non-restraint) = -10266.8730 + Ewald error estimate: 0.4142E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.854 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 283.14 PRESS = 0.0 + Etot = -8506.2197 EKtot = 1789.7840 EPtot = -10296.0037 + BOND = 23.2600 ANGLE = 77.1238 DIHED = 74.6823 + 1-4 NB = 31.2022 1-4 EEL = 514.4454 VDWAALS = 1406.5703 + EELEC = -12426.0523 EHBOND = 0.0000 RESTRAINT = 2.7645 + EAMBER (non-restraint) = -10298.7682 + Ewald error estimate: 0.4337E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 2.765 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 280.24 PRESS = 0.0 + Etot = -8505.1284 EKtot = 1771.4852 EPtot = -10276.6136 + BOND = 26.3807 ANGLE = 67.1346 DIHED = 76.7580 + 1-4 NB = 31.9009 1-4 EEL = 519.5149 VDWAALS = 1410.6846 + EELEC = -12411.7329 EHBOND = 0.0000 RESTRAINT = 2.7455 + EAMBER (non-restraint) = -10279.3591 + Ewald error estimate: 0.4092E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 2.745 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 285.52 PRESS = 0.0 + Etot = -8504.4859 EKtot = 1804.8271 EPtot = -10309.3129 + BOND = 25.8049 ANGLE = 69.7632 DIHED = 71.1631 + 1-4 NB = 29.8081 1-4 EEL = 524.5095 VDWAALS = 1405.2455 + EELEC = -12438.3290 EHBOND = 0.0000 RESTRAINT = 2.7217 + EAMBER (non-restraint) = -10312.0347 + Ewald error estimate: 0.2360E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 2.722 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 283.36 PRESS = 0.0 + Etot = -8503.4675 EKtot = 1791.1976 EPtot = -10294.6651 + BOND = 23.5705 ANGLE = 66.9791 DIHED = 72.4567 + 1-4 NB = 33.0260 1-4 EEL = 528.4085 VDWAALS = 1412.2146 + EELEC = -12434.0060 EHBOND = 0.0000 RESTRAINT = 2.6856 + EAMBER (non-restraint) = -10297.3506 + Ewald error estimate: 0.9501E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 2.686 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 281.46 PRESS = 0.0 + Etot = -8470.3960 EKtot = 1779.1542 EPtot = -10249.5502 + BOND = 25.7761 ANGLE = 55.8022 DIHED = 75.3272 + 1-4 NB = 34.0068 1-4 EEL = 534.2188 VDWAALS = 1442.9203 + EELEC = -12418.4273 EHBOND = 0.0000 RESTRAINT = 0.8258 + EAMBER (non-restraint) = -10250.3760 + Ewald error estimate: 0.7505E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.826 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 287.94 PRESS = 0.0 + Etot = -8470.1317 EKtot = 1820.1163 EPtot = -10290.2480 + BOND = 21.0300 ANGLE = 60.8428 DIHED = 78.6979 + 1-4 NB = 33.2464 1-4 EEL = 540.2732 VDWAALS = 1435.6969 + EELEC = -12460.8499 EHBOND = 0.0000 RESTRAINT = 0.8147 + EAMBER (non-restraint) = -10291.0627 + Ewald error estimate: 0.6979E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.815 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 282.37 PRESS = 0.0 + Etot = -8468.4104 EKtot = 1784.9530 EPtot = -10253.3634 + BOND = 29.4089 ANGLE = 51.1135 DIHED = 79.9810 + 1-4 NB = 32.3287 1-4 EEL = 541.0447 VDWAALS = 1433.8589 + EELEC = -12421.9006 EHBOND = 0.0000 RESTRAINT = 0.8015 + EAMBER (non-restraint) = -10254.1649 + Ewald error estimate: 0.2309E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.802 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 286.43 PRESS = 0.0 + Etot = -8468.0040 EKtot = 1810.5811 EPtot = -10278.5852 + BOND = 27.3024 ANGLE = 54.3433 DIHED = 76.9280 + 1-4 NB = 33.0109 1-4 EEL = 543.0536 VDWAALS = 1452.5261 + EELEC = -12466.5490 EHBOND = 0.0000 RESTRAINT = 0.7996 + EAMBER (non-restraint) = -10279.3848 + Ewald error estimate: 0.1823E-03 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.800 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 278.83 PRESS = 0.0 + Etot = -8495.0926 EKtot = 1762.5288 EPtot = -10257.6214 + BOND = 25.2470 ANGLE = 68.4638 DIHED = 72.4801 + 1-4 NB = 32.6143 1-4 EEL = 519.9378 VDWAALS = 1396.9670 + EELEC = -12375.8681 EHBOND = 0.0000 RESTRAINT = 2.5366 + EAMBER (non-restraint) = -10260.1580 + Ewald error estimate: 0.7212E-04 + TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 2.537 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines, Average for All Tasks: +| +| Routine Sec % +| ------------------------------ +| DataDistrib 0.01 1.02 +| Nonbond 1.01 93.75 +| Bond 0.00 0.05 +| Angle 0.00 0.28 +| Dihedral 0.00 0.46 +| Shake 0.00 0.19 +| RunMD 0.01 1.39 +| Other 0.03 2.87 +| ------------------------------ +| Total 1.08 + +| PME Nonbond Pairlist CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.28 +| Build List 0.20 18.42 +| --------------------------------- +| Total 0.20 18.70 + +| PME Direct Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.53 49.10 +| Exclude Masked 0.01 1.02 +| Other 0.01 1.11 +| --------------------------------- +| Total 0.55 51.23 + +| PME Reciprocal Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.03 2.59 +| Grid Charges 0.02 1.76 +| Scalar Sum 0.05 4.72 +| Gradient Sum 0.02 2.27 +| FFT 0.13 12.49 +| --------------------------------- +| Total 0.26 23.83 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 + +| Final Performance Info: +| ----------------------------------------------------- +| Average timings for last 45 steps: +| Elapsed(s) = 0.97 Per Step(ms) = 21.55 +| ns/day = 8.02 seconds/ns = 10774.73 +| +| Average timings for all steps: +| Elapsed(s) = 1.08 Per Step(ms) = 21.65 +| ns/day = 7.98 seconds/ns = 10824.85 +| ----------------------------------------------------- + +| Master Setup CPU time: 0.07 seconds +| Master NonSetup CPU time: 1.08 seconds +| Master Total CPU time: 1.15 seconds 0.00 hours + +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds +| Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/premd/save/mdout.2 test/nfe/premd/save/mdout.2 index 58f1ce8830..b9295e4dc5 100644 --- test/nfe/premd/save/mdout.2 +++ test/nfe/premd/save/mdout.2 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/14/2016 at 17:59:34 +| Run on 09/21/2018 at 19:24:35 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/premd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/premd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -45,9 +45,9 @@ File Assignments: ntb = 1, ntp = 0, temp0 = 310.0, ntt = 1, gamma_ln = 0.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, - numexchg = 10, infe = 1, + numexchg = 10, infe = 1, / &pmd @@ -83,8 +83,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -106,7 +106,7 @@ General flags: imin = 0, nmropt = 0 Replica exchange - numexchg= 10, rem= 1 + numexchg= 10, rem= 3 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 @@ -157,18 +157,35 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + NFE : + NFE : output_file = pmd.2.txt + NFE : output_freq = 1 (0.0020 ps) + NFE : + NFE : CV #1 << anchor : position = 1.000000, 6.000000, 6.000000, 11.000000 + NFE : strength = 2.000000, 2.000000 >> + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + | # of SOLUTE degrees of freedom (RNDFP): 6365. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 6362. NUM_NOSHAKE = 0 CORRECTED RNDFP = 6362. @@ -180,158 +197,203 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 651699 +| Local SIZE OF NONBOND LIST = 330734 | TOTAL SIZE OF NONBOND LIST = 651699 - NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 295.33 PRESS = 0.0 - Etot = -8450.1398 EKtot = 1866.8462 EPtot = -10316.9860 - BOND = 28.8217 ANGLE = 67.8604 DIHED = 69.9709 - 1-4 NB = 30.8337 1-4 EEL = 509.2117 VDWAALS = 1394.8433 - EELEC = -12418.5276 EHBOND = 0.0000 RESTRAINT = 0.0000 + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 295.40 PRESS = 0.0 + Etot = -8447.7854 EKtot = 1867.3028 EPtot = -10315.0882 + BOND = 28.8232 ANGLE = 67.8660 DIHED = 69.9719 + 1-4 NB = 30.8343 1-4 EEL = 509.2122 VDWAALS = 1394.8478 + EELEC = -12418.4943 EHBOND = 0.0000 RESTRAINT = 1.8507 + EAMBER (non-restraint) = -10316.9389 Ewald error estimate: 0.5046E-03 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 1 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 1 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 289.65 PRESS = 0.0 - Etot = -8449.5038 EKtot = 1830.9270 EPtot = -10280.4308 - BOND = 23.5883 ANGLE = 78.1864 DIHED = 75.0311 - 1-4 NB = 31.2570 1-4 EEL = 514.4759 VDWAALS = 1408.9030 - EELEC = -12411.8725 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4293E-03 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 2 + NFE restraints: SMD : 0.000 PMD : 1.851 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 287.13 PRESS = 0.0 + Etot = -8417.0148 EKtot = 1815.0052 EPtot = -10232.0199 + BOND = 28.3778 ANGLE = 66.0921 DIHED = 84.3965 + 1-4 NB = 29.7633 1-4 EEL = 534.7789 VDWAALS = 1434.0510 + EELEC = -12409.5715 EHBOND = 0.0000 RESTRAINT = 0.0921 + EAMBER (non-restraint) = -10232.1120 + Ewald error estimate: 0.3385E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 2 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 285.00 PRESS = 0.0 - Etot = -8448.7576 EKtot = 1801.5303 EPtot = -10250.2879 - BOND = 26.6984 ANGLE = 68.0428 DIHED = 77.0257 - 1-4 NB = 32.0001 1-4 EEL = 519.5401 VDWAALS = 1417.7911 - EELEC = -12391.3862 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3788E-03 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 3 + NFE restraints: SMD : 0.000 PMD : 0.092 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 282.48 PRESS = 0.0 + Etot = -8415.4792 EKtot = 1785.5988 EPtot = -10201.0780 + BOND = 29.8610 ANGLE = 62.2784 DIHED = 83.0387 + 1-4 NB = 28.8017 1-4 EEL = 528.8488 VDWAALS = 1445.1848 + EELEC = -12379.1831 EHBOND = 0.0000 RESTRAINT = 0.0917 + EAMBER (non-restraint) = -10201.1697 + Ewald error estimate: 0.2653E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 3 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 290.54 PRESS = 0.0 - Etot = -8448.4493 EKtot = 1836.5508 EPtot = -10285.0001 - BOND = 26.1256 ANGLE = 70.7433 DIHED = 71.3575 - 1-4 NB = 29.9031 1-4 EEL = 524.5637 VDWAALS = 1415.0188 - EELEC = -12422.7120 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1791E-03 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 4 + NFE restraints: SMD : 0.000 PMD : 0.092 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 283.69 PRESS = 0.0 + Etot = -8413.7163 EKtot = 1793.2996 EPtot = -10207.0159 + BOND = 33.5475 ANGLE = 68.2571 DIHED = 77.9961 + 1-4 NB = 30.6251 1-4 EEL = 536.8176 VDWAALS = 1444.3070 + EELEC = -12398.6542 EHBOND = 0.0000 RESTRAINT = 0.0879 + EAMBER (non-restraint) = -10207.1038 + Ewald error estimate: 0.2484E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 4 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 288.34 PRESS = 0.0 - Etot = -8447.7223 EKtot = 1822.6492 EPtot = -10270.3715 - BOND = 23.8838 ANGLE = 67.7601 DIHED = 72.8046 - 1-4 NB = 33.1648 1-4 EEL = 528.4536 VDWAALS = 1421.9664 - EELEC = -12418.4048 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3989E-04 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 5 + NFE restraints: SMD : 0.000 PMD : 0.088 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 290.14 PRESS = 0.0 + Etot = -8413.4655 EKtot = 1834.0312 EPtot = -10247.4967 + BOND = 24.4121 ANGLE = 58.0324 DIHED = 82.0070 + 1-4 NB = 32.4143 1-4 EEL = 536.9822 VDWAALS = 1445.6388 + EELEC = -12427.0683 EHBOND = 0.0000 RESTRAINT = 0.0850 + EAMBER (non-restraint) = -10247.5817 + Ewald error estimate: 0.1466E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 5 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 283.39 PRESS = 0.0 - Etot = -8446.6196 EKtot = 1791.4084 EPtot = -10238.0280 - BOND = 18.3622 ANGLE = 74.9667 DIHED = 69.7724 - 1-4 NB = 31.4293 1-4 EEL = 524.7582 VDWAALS = 1439.5697 - EELEC = -12396.8865 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3986E-04 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 6 + NFE restraints: SMD : 0.000 PMD : 0.085 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 285.46 PRESS = 0.0 + Etot = -8443.3623 EKtot = 1804.4675 EPtot = -10247.8298 + BOND = 18.3572 ANGLE = 75.1744 DIHED = 69.8160 + 1-4 NB = 31.3716 1-4 EEL = 524.6978 VDWAALS = 1434.2832 + EELEC = -12403.2170 EHBOND = 0.0000 RESTRAINT = 1.6870 + EAMBER (non-restraint) = -10249.5168 + Ewald error estimate: 0.2096E-04 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 6 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 283.51 PRESS = 0.0 - Etot = -8445.5408 EKtot = 1792.1292 EPtot = -10237.6700 - BOND = 19.5930 ANGLE = 63.2416 DIHED = 78.0756 - 1-4 NB = 30.8307 1-4 EEL = 525.2646 VDWAALS = 1433.7331 - EELEC = -12388.4086 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2654E-04 - TEMP0 = 300.0000 REPNUM = 2 EXCHANGE# = 7 + NFE restraints: SMD : 0.000 PMD : 1.687 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 283.99 PRESS = 0.0 + Etot = -8441.7377 EKtot = 1795.1826 EPtot = -10236.9203 + BOND = 19.6145 ANGLE = 63.3477 DIHED = 78.0255 + 1-4 NB = 30.8063 1-4 EEL = 525.2769 VDWAALS = 1436.2897 + EELEC = -12391.9259 EHBOND = 0.0000 RESTRAINT = 1.6449 + EAMBER (non-restraint) = -10238.5653 + Ewald error estimate: 0.1519E-04 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 7 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 292.68 PRESS = 0.0 - Etot = -8384.5700 EKtot = 1850.1242 EPtot = -10234.6942 - BOND = 28.5032 ANGLE = 68.9322 DIHED = 77.2102 - 1-4 NB = 28.5730 1-4 EEL = 524.6359 VDWAALS = 1426.6991 - EELEC = -12389.2478 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2911E-04 + NFE restraints: SMD : 0.000 PMD : 1.645 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 286.97 PRESS = 0.0 + Etot = -8440.3552 EKtot = 1813.9828 EPtot = -10254.3380 + BOND = 28.0799 ANGLE = 68.2327 DIHED = 76.7471 + 1-4 NB = 28.5123 1-4 EEL = 524.6904 VDWAALS = 1432.3317 + EELEC = -12414.5442 EHBOND = 0.0000 RESTRAINT = 1.6122 + EAMBER (non-restraint) = -10255.9502 + Ewald error estimate: 0.1051E-04 TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 8 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 290.34 PRESS = 0.0 - Etot = -8383.2758 EKtot = 1835.3241 EPtot = -10218.5998 - BOND = 25.6749 ANGLE = 76.0302 DIHED = 70.9279 - 1-4 NB = 30.7081 1-4 EEL = 519.0225 VDWAALS = 1420.2275 - EELEC = -12361.1910 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3740E-05 + NFE restraints: SMD : 0.000 PMD : 1.612 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 286.30 PRESS = 0.0 + Etot = -8438.7388 EKtot = 1809.8062 EPtot = -10248.5449 + BOND = 25.3239 ANGLE = 75.0334 DIHED = 70.7730 + 1-4 NB = 30.6675 1-4 EEL = 519.1729 VDWAALS = 1422.4925 + EELEC = -12393.5980 EHBOND = 0.0000 RESTRAINT = 1.5900 + EAMBER (non-restraint) = -10250.1349 + Ewald error estimate: 0.4209E-04 TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 9 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 289.40 PRESS = 0.0 - Etot = -8382.1131 EKtot = 1829.3586 EPtot = -10211.4717 - BOND = 25.9605 ANGLE = 70.3144 DIHED = 73.1317 - 1-4 NB = 32.8286 1-4 EEL = 519.6907 VDWAALS = 1399.6607 - EELEC = -12333.0584 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5959E-04 + NFE restraints: SMD : 0.000 PMD : 1.590 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 286.00 PRESS = 0.0 + Etot = -8405.8616 EKtot = 1807.8849 EPtot = -10213.7465 + BOND = 32.7170 ANGLE = 62.8508 DIHED = 76.7827 + 1-4 NB = 35.1790 1-4 EEL = 540.1667 VDWAALS = 1484.6222 + EELEC = -12446.1363 EHBOND = 0.0000 RESTRAINT = 0.0713 + EAMBER (non-restraint) = -10213.8177 + Ewald error estimate: 0.1971E-03 TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 10 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.071 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.30% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.27% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.29 (90.86% of List ) -| Other 0.03 ( 9.14% of List ) -| List time 0.32 ( 9.59% of Nonbo) -| Short_ene time 2.28 (99.16% of Direc) -| Other 0.02 ( 0.84% of Direc) -| Direct Ewald time 2.30 (76.66% of Ewald) -| Adjust Ewald time 0.02 ( 0.62% of Ewald) +| Build the list 0.46 (95.57% of List ) +| Other 0.02 ( 4.43% of List ) +| List time 0.49 (23.59% of Nonbo) +| Short_ene time 0.94 (97.95% of Direc) +| Other 0.02 ( 2.05% of Direc) +| Direct Ewald time 0.96 (61.32% of Ewald) +| Adjust Ewald time 0.01 ( 0.44% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.03 ( 4.10% of Recip) -| Fill charge grid 0.05 ( 7.33% of Recip) -| Scalar sum 0.28 (41.60% of Recip) -| Grad sum 0.11 (16.02% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.21 (100.0% of FFT t) -| FFT time 0.21 (30.92% of Recip) -| Other 0.00 ( 0.03% of Recip) -| Recip Ewald time 0.68 (22.58% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.04% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 3.01 (90.41% of Nonbo) -| Nonbond force 3.32 (98.92% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.47% of Force) -| Other 0.02 ( 0.60% of Force) -| Force time 3.36 (94.34% of Runmd) -| Shake time 0.02 ( 0.47% of Runmd) -| Verlet update time 0.01 ( 0.37% of Runmd) -| Other 0.17 ( 4.83% of Runmd) -| Runmd Time 3.56 (98.32% of Total) -| Other 0.05 ( 1.37% of Total) -| Total time 3.62 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Fill Bspline coeffs 0.02 ( 5.29% of Recip) +| Fill charge grid 0.02 ( 6.14% of Recip) +| Scalar sum 0.10 (24.99% of Recip) +| Grad sum 0.05 (13.63% of Recip) +| FFT back comm time 0.01 ( 7.22% of FFT t) +| Other 0.16 (92.78% of FFT t) +| FFT time 0.17 (42.75% of Recip) +| Other 0.03 ( 7.19% of Recip) +| Recip Ewald time 0.40 (25.58% of Ewald) +| Force Adjust 0.20 (12.47% of Ewald) +| Virial junk 0.00 ( 0.12% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.57 (76.41% of Nonbo) +| Nonbond force 2.06 (99.34% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.34% of Force) +| FRC Collect time 0.00 ( 0.12% of Force) +| Other 0.00 ( 0.20% of Force) +| Force time 2.07 (96.66% of Runmd) +| Shake time 0.00 ( 0.22% of Runmd) +| Verlet update time 0.01 ( 0.35% of Runmd) +| CRD distribute time 0.00 ( 0.03% of Runmd) +| Other 0.06 ( 2.74% of Runmd) +| Runmd Time 2.14 (97.11% of Total) +| Other 0.06 ( 2.61% of Total) +| Total time 2.21 (100.0% of ALL ) + +| Number of list builds : 18 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 3.56 Per Step(ms) = 71.25 -| ns/day = 2.43 seconds/ns = 35622.87 +| Elapsed(s) = 2.14 Per Step(ms) = 42.87 +| ns/day = 4.03 seconds/ns = 21434.79 | ----------------------------------------------------- -| Job began at 17:59:34.530 on 06/14/2016 -| Setup done at 17:59:34.592 on 06/14/2016 -| Run done at 17:59:38.154 on 06/14/2016 -| wallclock() was called 3211 times +| Job began at 19:24:35.570 on 09/21/2018 +| Setup done at 19:24:35.635 on 09/21/2018 +| Run done at 19:24:37.778 on 09/21/2018 +| wallclock() was called 3777 times diff --git test/nfe/premd/save/mdout.2.pmemd test/nfe/premd/save/mdout.2.pmemd new file mode 100644 index 0000000000..caa8fc19bc --- /dev/null +++ test/nfe/premd/save/mdout.2.pmemd @@ -0,0 +1,429 @@ + + ------------------------------------------------------- + Amber 18 PMEMD 2018 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 18 + +| Run on 09/21/2018 at 19:25:45 + +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/premd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output + +File Assignments: +| MDIN: mdin.2 +| MDOUT: mdout.2 +| INPCRD: inpcrd.2 +| PARM: prmtop +| RESTRT: restrt.2 +| REFC: refc +| MDVEL: mdvel.001 +| MDEN: mden.001 +| MDCRD: mdcrd.2 +| MDINFO: /dev/null +|LOGFILE: logfile.001 +| MDFRC: mdfrc.001 + + + Here is the input file: + + + &cntrl + igb = 0, ntx = 7, irest = 1, + ntb = 1, ntp = 0, temp0 = 310.0, + ntt = 1, gamma_ln = 0.0, + ntf = 2, ntc = 2, tol = 0.00001, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, + numexchg = 10, infe = 1, + / + + &pmd + output_file = 'pmd.2.txt' + output_freq = 1 + cv_file = 'cv.2' + / + + +| irandom = 1, using AMBER's internal random number generator (default). + + +| Conditional Compilation Defines Used: +| MPI +| PUBFFT +| BINTRAJ +| EMIL + +| Largest sphere to fit in unit cell has radius = 14.075 + +| New format PARM file being parsed. +| Version = 1.000 Date = 09/01/07 Time = 11:29:05 + +| Note: 1-4 EEL scale factors were NOT found in the topology file. +| Using default value of 1.2. + +| Note: 1-4 VDW scale factors were NOT found in the topology file. +| Using default value of 2.0. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 + NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 + NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 + NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 + NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 + IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 6 6 6 +| Direct force subcell size = 5.7460 5.7460 5.7460 + + BOX TYPE: TRUNCATED OCTAHEDRON + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + +NGLY + +General flags: + imin = 0, nmropt = 0 + +Replica exchange + numexchg= 10, rem= 3 + +Nature and format of input: + ntx = 7, irest = 1, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 5, ntrx = 1, ntwr = 50 + iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 2, ntb = 1, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 0 + +Molecular dynamics: + nstlim = 5, nscm = 1000, nrespa = 1 + t = 0.00000, dt = 0.00200, vlimit = 20.00000 + +Berendsen (weak-coupling) temperature regulation: + temp0 = 310.00000, tempi = 0.00000, tautp = 1.00000 + +SHAKE: + ntc = 2, jfastw = 0 + tol = 0.00001 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 5 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 1 + Box X = 34.476 Box Y = 34.476 Box Z = 34.476 + Alpha = 109.471 Beta = 109.471 Gamma = 109.471 + NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + +NGLY + begin time read from input coords = 0.000 ps + + + Number of triangulated 3-point waters found: 1001 + + Sum of charges from parm topology file = -0.00000001 + Forcing neutrality... + +| Dynamic Memory, Types Used: +| Reals 245722 +| Integers 210813 + +| Nonbonded Pairs Initial Allocation: 358302 + +| Running AMBER/MPI version on 2 MPI task + + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + --------------------------------------------------- + APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION + using 5000.0 points per unit in tabled values + TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff +| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 +| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 + --------------------------------------------------- +|--------------------------------------------------- +| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.47 +| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.89 +|--------------------------------------------------- + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + NFE : + NFE : output_file = pmd.2.txt + NFE : output_freq = 1 (0.0020 ps) + NFE : + NFE : CV #1 << anchor : position = 1.000000, 6.000000, 6.000000, 11.000000 + NFE : strength = 2.000000, 2.000000 >> + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + + + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 295.40 PRESS = 0.0 + Etot = -8447.7854 EKtot = 1867.3028 EPtot = -10315.0882 + BOND = 28.8232 ANGLE = 67.8660 DIHED = 69.9719 + 1-4 NB = 30.8343 1-4 EEL = 509.2122 VDWAALS = 1394.8478 + EELEC = -12418.4943 EHBOND = 0.0000 RESTRAINT = 1.8507 + EAMBER (non-restraint) = -10316.9389 + Ewald error estimate: 0.5046E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 1.851 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 287.13 PRESS = 0.0 + Etot = -8417.0148 EKtot = 1815.0052 EPtot = -10232.0199 + BOND = 28.3778 ANGLE = 66.0921 DIHED = 84.3965 + 1-4 NB = 29.7633 1-4 EEL = 534.7789 VDWAALS = 1434.0510 + EELEC = -12409.5715 EHBOND = 0.0000 RESTRAINT = 0.0921 + EAMBER (non-restraint) = -10232.1120 + Ewald error estimate: 0.3385E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.092 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 282.48 PRESS = 0.0 + Etot = -8415.4792 EKtot = 1785.5988 EPtot = -10201.0780 + BOND = 29.8610 ANGLE = 62.2784 DIHED = 83.0387 + 1-4 NB = 28.8017 1-4 EEL = 528.8488 VDWAALS = 1445.1848 + EELEC = -12379.1831 EHBOND = 0.0000 RESTRAINT = 0.0917 + EAMBER (non-restraint) = -10201.1697 + Ewald error estimate: 0.2653E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.092 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 283.69 PRESS = 0.0 + Etot = -8413.7163 EKtot = 1793.2996 EPtot = -10207.0159 + BOND = 33.5475 ANGLE = 68.2571 DIHED = 77.9961 + 1-4 NB = 30.6251 1-4 EEL = 536.8176 VDWAALS = 1444.3070 + EELEC = -12398.6542 EHBOND = 0.0000 RESTRAINT = 0.0879 + EAMBER (non-restraint) = -10207.1038 + Ewald error estimate: 0.2484E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.088 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 290.14 PRESS = 0.0 + Etot = -8413.4655 EKtot = 1834.0312 EPtot = -10247.4967 + BOND = 24.4121 ANGLE = 58.0324 DIHED = 82.0070 + 1-4 NB = 32.4143 1-4 EEL = 536.9822 VDWAALS = 1445.6388 + EELEC = -12427.0683 EHBOND = 0.0000 RESTRAINT = 0.0850 + EAMBER (non-restraint) = -10247.5817 + Ewald error estimate: 0.1466E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.085 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 285.46 PRESS = 0.0 + Etot = -8443.3623 EKtot = 1804.4675 EPtot = -10247.8298 + BOND = 18.3572 ANGLE = 75.1744 DIHED = 69.8160 + 1-4 NB = 31.3716 1-4 EEL = 524.6978 VDWAALS = 1434.2832 + EELEC = -12403.2170 EHBOND = 0.0000 RESTRAINT = 1.6870 + EAMBER (non-restraint) = -10249.5168 + Ewald error estimate: 0.2096E-04 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 1.687 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 283.99 PRESS = 0.0 + Etot = -8441.7377 EKtot = 1795.1826 EPtot = -10236.9203 + BOND = 19.6145 ANGLE = 63.3477 DIHED = 78.0255 + 1-4 NB = 30.8063 1-4 EEL = 525.2769 VDWAALS = 1436.2897 + EELEC = -12391.9259 EHBOND = 0.0000 RESTRAINT = 1.6449 + EAMBER (non-restraint) = -10238.5653 + Ewald error estimate: 0.1519E-04 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 1.645 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 286.97 PRESS = 0.0 + Etot = -8440.3552 EKtot = 1813.9828 EPtot = -10254.3380 + BOND = 28.0799 ANGLE = 68.2327 DIHED = 76.7471 + 1-4 NB = 28.5123 1-4 EEL = 524.6904 VDWAALS = 1432.3317 + EELEC = -12414.5442 EHBOND = 0.0000 RESTRAINT = 1.6122 + EAMBER (non-restraint) = -10255.9502 + Ewald error estimate: 0.1051E-04 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 1.612 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 286.30 PRESS = 0.0 + Etot = -8438.7388 EKtot = 1809.8062 EPtot = -10248.5449 + BOND = 25.3239 ANGLE = 75.0334 DIHED = 70.7730 + 1-4 NB = 30.6675 1-4 EEL = 519.1729 VDWAALS = 1422.4925 + EELEC = -12393.5980 EHBOND = 0.0000 RESTRAINT = 1.5900 + EAMBER (non-restraint) = -10250.1349 + Ewald error estimate: 0.4209E-04 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 1.590 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 286.00 PRESS = 0.0 + Etot = -8405.8616 EKtot = 1807.8849 EPtot = -10213.7465 + BOND = 32.7170 ANGLE = 62.8508 DIHED = 76.7827 + 1-4 NB = 35.1790 1-4 EEL = 540.1667 VDWAALS = 1484.6222 + EELEC = -12446.1363 EHBOND = 0.0000 RESTRAINT = 0.0713 + EAMBER (non-restraint) = -10213.8177 + Ewald error estimate: 0.1971E-03 + TEMP0 = 310.0000 REPNUM = 2 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.071 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines, Average for All Tasks: +| +| Routine Sec % +| ------------------------------ +| DataDistrib 0.01 1.02 +| Nonbond 1.02 94.68 +| Bond 0.00 0.00 +| Angle 0.00 0.14 +| Dihedral 0.01 0.65 +| Shake 0.00 0.18 +| RunMD 0.01 1.34 +| Other 0.02 1.99 +| ------------------------------ +| Total 1.08 + +| PME Nonbond Pairlist CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.23 +| Build List 0.21 19.70 +| --------------------------------- +| Total 0.22 19.94 + +| PME Direct Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.53 49.03 +| Exclude Masked 0.01 1.16 +| Other 0.01 0.97 +| --------------------------------- +| Total 0.55 51.16 + +| PME Reciprocal Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.03 2.77 +| Grid Charges 0.02 1.57 +| Scalar Sum 0.05 4.72 +| Gradient Sum 0.02 2.22 +| FFT 0.13 12.30 +| --------------------------------- +| Total 0.25 23.59 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 + +| Final Performance Info: +| ----------------------------------------------------- +| Average timings for last 45 steps: +| Elapsed(s) = 0.96 Per Step(ms) = 21.30 +| ns/day = 8.11 seconds/ns = 10649.76 +| +| Average timings for all steps: +| Elapsed(s) = 1.08 Per Step(ms) = 21.65 +| ns/day = 7.98 seconds/ns = 10826.00 +| ----------------------------------------------------- + +| Master Setup CPU time: 0.07 seconds +| Master NonSetup CPU time: 1.08 seconds +| Master Total CPU time: 1.15 seconds 0.00 hours + +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds +| Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/premd/save/mdout.3 test/nfe/premd/save/mdout.3 index 165f89b1c3..5967ae7c58 100644 --- test/nfe/premd/save/mdout.3 +++ test/nfe/premd/save/mdout.3 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/14/2016 at 17:59:34 +| Run on 09/21/2018 at 19:24:35 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/premd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/premd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -45,9 +45,9 @@ File Assignments: ntb = 1, ntp = 0, temp0 = 320.0, ntt = 1, gamma_ln = 0.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, - numexchg = 10, infe = 1, + numexchg = 10, infe = 1, / &pmd @@ -83,8 +83,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -106,7 +106,7 @@ General flags: imin = 0, nmropt = 0 Replica exchange - numexchg= 10, rem= 1 + numexchg= 10, rem= 3 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 @@ -157,18 +157,35 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + NFE : + NFE : output_file = pmd.3.txt + NFE : output_freq = 1 (0.0020 ps) + NFE : + NFE : CV #1 << anchor : position = 2.000000, 7.000000, 7.000000, 12.000000 + NFE : strength = 3.000000, 3.000000 >> + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + | # of SOLUTE degrees of freedom (RNDFP): 6365. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 6362. NUM_NOSHAKE = 0 CORRECTED RNDFP = 6362. @@ -180,158 +197,203 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 650919 +| Local SIZE OF NONBOND LIST = 328843 | TOTAL SIZE OF NONBOND LIST = 650919 - NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 309.55 PRESS = 0.0 - Etot = -8149.4151 EKtot = 1956.7173 EPtot = -10106.1325 - BOND = 27.8429 ANGLE = 67.0129 DIHED = 74.1065 - 1-4 NB = 29.5941 1-4 EEL = 526.8767 VDWAALS = 1332.7251 - EELEC = -12164.2906 EHBOND = 0.0000 RESTRAINT = 0.0000 + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 309.47 PRESS = 0.0 + Etot = -8148.3747 EKtot = 1956.2272 EPtot = -10104.6019 + BOND = 27.8338 ANGLE = 67.0127 DIHED = 74.1063 + 1-4 NB = 29.5980 1-4 EEL = 526.8812 VDWAALS = 1332.7204 + EELEC = -12164.3317 EHBOND = 0.0000 RESTRAINT = 1.5773 + EAMBER (non-restraint) = -10106.1793 Ewald error estimate: 0.2771E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 1 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 1 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.44 PRESS = 0.0 - Etot = -8147.5650 EKtot = 1918.1137 EPtot = -10065.6787 - BOND = 33.2309 ANGLE = 59.4210 DIHED = 77.5536 - 1-4 NB = 31.0387 1-4 EEL = 525.2555 VDWAALS = 1340.9469 - EELEC = -12133.1253 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.8884E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 2 + NFE restraints: SMD : 0.000 PMD : 1.577 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 318.24 PRESS = 0.0 + Etot = -8057.8055 EKtot = 2011.6624 EPtot = -10069.4678 + BOND = 31.4275 ANGLE = 73.8749 DIHED = 78.6156 + 1-4 NB = 33.3465 1-4 EEL = 533.7908 VDWAALS = 1430.6460 + EELEC = -12251.5089 EHBOND = 0.0000 RESTRAINT = 0.3397 + EAMBER (non-restraint) = -10069.8075 + Ewald error estimate: 0.4813E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 2 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 307.50 PRESS = 0.0 - Etot = -8146.9494 EKtot = 1943.7623 EPtot = -10090.7117 - BOND = 34.3107 ANGLE = 57.3683 DIHED = 76.4441 - 1-4 NB = 29.1374 1-4 EEL = 521.0165 VDWAALS = 1331.2796 - EELEC = -12140.2683 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1331E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 3 + NFE restraints: SMD : 0.000 PMD : 0.340 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 325.08 PRESS = 0.0 + Etot = -8058.2731 EKtot = 2054.8859 EPtot = -10113.1590 + BOND = 23.6875 ANGLE = 74.1512 DIHED = 73.1603 + 1-4 NB = 32.6120 1-4 EEL = 540.9514 VDWAALS = 1436.6876 + EELEC = -12294.7403 EHBOND = 0.0000 RESTRAINT = 0.3312 + EAMBER (non-restraint) = -10113.4902 + Ewald error estimate: 0.2507E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 3 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 304.21 PRESS = 0.0 - Etot = -8144.8139 EKtot = 1922.9940 EPtot = -10067.8080 - BOND = 27.6844 ANGLE = 62.4242 DIHED = 77.4778 - 1-4 NB = 31.6423 1-4 EEL = 522.4895 VDWAALS = 1309.8288 - EELEC = -12099.3549 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4818E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 4 + NFE restraints: SMD : 0.000 PMD : 0.331 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 320.24 PRESS = 0.0 + Etot = -8057.7688 EKtot = 2024.3408 EPtot = -10082.1096 + BOND = 31.5904 ANGLE = 76.3049 DIHED = 76.3418 + 1-4 NB = 35.7187 1-4 EEL = 541.8974 VDWAALS = 1427.1453 + EELEC = -12271.4222 EHBOND = 0.0000 RESTRAINT = 0.3141 + EAMBER (non-restraint) = -10082.4238 + Ewald error estimate: 0.1687E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 4 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 310.27 PRESS = 0.0 - Etot = -8143.9027 EKtot = 1961.2870 EPtot = -10105.1897 - BOND = 23.0027 ANGLE = 68.1563 DIHED = 72.9903 - 1-4 NB = 30.7702 1-4 EEL = 523.2612 VDWAALS = 1292.6995 - EELEC = -12116.0699 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4373E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 5 + NFE restraints: SMD : 0.000 PMD : 0.314 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 317.56 PRESS = 0.0 + Etot = -8057.6238 EKtot = 2007.3881 EPtot = -10065.0119 + BOND = 31.8921 ANGLE = 62.2308 DIHED = 79.9793 + 1-4 NB = 32.7820 1-4 EEL = 541.2369 VDWAALS = 1427.3876 + EELEC = -12240.8164 EHBOND = 0.0000 RESTRAINT = 0.2957 + EAMBER (non-restraint) = -10065.3076 + Ewald error estimate: 0.1090E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 5 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 306.46 PRESS = 0.0 - Etot = -8141.8283 EKtot = 1937.2305 EPtot = -10079.0588 - BOND = 37.1791 ANGLE = 66.3705 DIHED = 75.4143 - 1-4 NB = 31.4229 1-4 EEL = 515.9433 VDWAALS = 1277.6942 - EELEC = -12083.0831 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.5787E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 6 + NFE restraints: SMD : 0.000 PMD : 0.296 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 311.55 PRESS = 0.0 + Etot = -8057.4936 EKtot = 1969.3841 EPtot = -10026.8778 + BOND = 32.6072 ANGLE = 63.3747 DIHED = 83.3507 + 1-4 NB = 35.2471 1-4 EEL = 538.1261 VDWAALS = 1445.3751 + EELEC = -12225.2337 EHBOND = 0.0000 RESTRAINT = 0.2752 + EAMBER (non-restraint) = -10027.1529 + Ewald error estimate: 0.6948E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 6 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 308.20 PRESS = 0.0 - Etot = -8141.0483 EKtot = 1948.2084 EPtot = -10089.2566 - BOND = 18.2612 ANGLE = 61.4358 DIHED = 79.8681 - 1-4 NB = 31.5707 1-4 EEL = 535.3154 VDWAALS = 1258.6299 - EELEC = -12074.3378 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1197E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 7 + NFE restraints: SMD : 0.000 PMD : 0.275 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 308.98 PRESS = 0.0 + Etot = -8057.3530 EKtot = 1953.1512 EPtot = -10010.5042 + BOND = 31.2338 ANGLE = 63.2499 DIHED = 77.8451 + 1-4 NB = 36.3124 1-4 EEL = 542.0073 VDWAALS = 1437.6859 + EELEC = -12199.0961 EHBOND = 0.0000 RESTRAINT = 0.2575 + EAMBER (non-restraint) = -10010.7617 + Ewald error estimate: 0.3057E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 7 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 311.45 PRESS = 0.0 - Etot = -8139.8204 EKtot = 1968.7642 EPtot = -10108.5847 - BOND = 24.1915 ANGLE = 60.9784 DIHED = 76.3516 - 1-4 NB = 32.7424 1-4 EEL = 533.8674 VDWAALS = 1248.8229 - EELEC = -12085.5389 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3394E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 8 + NFE restraints: SMD : 0.000 PMD : 0.258 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 304.92 PRESS = 0.0 + Etot = -8056.4911 EKtot = 1927.4777 EPtot = -9983.9688 + BOND = 22.8244 ANGLE = 71.3503 DIHED = 78.0854 + 1-4 NB = 39.4656 1-4 EEL = 536.4455 VDWAALS = 1384.1603 + EELEC = -12116.5424 EHBOND = 0.0000 RESTRAINT = 0.2420 + EAMBER (non-restraint) = -9984.2108 + Ewald error estimate: 0.1498E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 8 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 309.27 PRESS = 0.0 - Etot = -8138.2769 EKtot = 1954.9868 EPtot = -10093.2636 - BOND = 33.9803 ANGLE = 67.1339 DIHED = 71.0929 - 1-4 NB = 29.6248 1-4 EEL = 529.4272 VDWAALS = 1267.7570 - EELEC = -12092.2797 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4759E-04 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 9 + NFE restraints: SMD : 0.000 PMD : 0.242 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 307.51 PRESS = 0.0 + Etot = -8055.7214 EKtot = 1943.8395 EPtot = -9999.5609 + BOND = 26.0709 ANGLE = 76.0954 DIHED = 77.2167 + 1-4 NB = 39.1124 1-4 EEL = 537.5107 VDWAALS = 1322.3124 + EELEC = -12078.1173 EHBOND = 0.0000 RESTRAINT = 0.2379 + EAMBER (non-restraint) = -9999.7988 + Ewald error estimate: 0.2664E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 9 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 307.41 PRESS = 0.0 - Etot = -8136.6805 EKtot = 1943.2325 EPtot = -10079.9130 - BOND = 27.3453 ANGLE = 63.4674 DIHED = 76.9752 - 1-4 NB = 33.9451 1-4 EEL = 541.9555 VDWAALS = 1312.1733 - EELEC = -12135.7748 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1561E-03 - TEMP0 = 330.0000 REPNUM = 3 EXCHANGE# = 10 + NFE restraints: SMD : 0.000 PMD : 0.238 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 315.45 PRESS = 0.0 + Etot = -8055.7951 EKtot = 1994.0534 EPtot = -10049.8485 + BOND = 24.9537 ANGLE = 67.7324 DIHED = 72.2504 + 1-4 NB = 34.9957 1-4 EEL = 539.6617 VDWAALS = 1296.1682 + EELEC = -12085.8453 EHBOND = 0.0000 RESTRAINT = 0.2346 + EAMBER (non-restraint) = -10050.0832 + Ewald error estimate: 0.3133E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 10 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.235 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.30% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.27% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.30 (91.09% of List ) -| Other 0.03 ( 8.91% of List ) -| List time 0.33 ( 9.60% of Nonbo) -| Short_ene time 2.34 (99.12% of Direc) -| Other 0.02 ( 0.88% of Direc) -| Direct Ewald time 2.36 (77.03% of Ewald) -| Adjust Ewald time 0.02 ( 0.62% of Ewald) +| Build the list 0.51 (95.91% of List ) +| Other 0.02 ( 4.09% of List ) +| List time 0.53 (25.38% of Nonbo) +| Short_ene time 1.12 (97.93% of Direc) +| Other 0.02 ( 2.07% of Direc) +| Direct Ewald time 1.14 (72.96% of Ewald) +| Adjust Ewald time 0.01 ( 0.53% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.03 ( 4.44% of Recip) -| Fill charge grid 0.05 ( 7.42% of Recip) -| Scalar sum 0.28 (40.69% of Recip) -| Grad sum 0.11 (16.33% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.21 (100.0% of FFT t) -| FFT time 0.21 (31.10% of Recip) -| Other 0.00 ( 0.03% of Recip) -| Recip Ewald time 0.68 (22.21% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.04% of Ewald) +| Fill Bspline coeffs 0.03 ( 6.75% of Recip) +| Fill charge grid 0.03 ( 7.79% of Recip) +| Scalar sum 0.12 (29.47% of Recip) +| Grad sum 0.07 (17.95% of Recip) +| FFT back comm time 0.01 ( 8.91% of FFT t) +| Other 0.14 (91.09% of FFT t) +| FFT time 0.15 (37.59% of Recip) +| Other 0.00 ( 0.45% of Recip) +| Recip Ewald time 0.40 (25.70% of Ewald) +| Force Adjust 0.01 ( 0.59% of Ewald) +| Virial junk 0.00 ( 0.14% of Ewald) | Other 0.00 ( 0.07% of Ewald) -| Ewald time 3.06 (90.39% of Nonbo) -| Nonbond force 3.38 (98.78% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.45% of Force) -| Other 0.03 ( 0.76% of Force) -| Force time 3.43 (95.94% of Runmd) -| Shake time 0.02 ( 0.47% of Runmd) -| Verlet update time 0.01 ( 0.37% of Runmd) -| Other 0.12 ( 3.23% of Runmd) -| Runmd Time 3.57 (98.32% of Total) -| Other 0.05 ( 1.37% of Total) -| Total time 3.63 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Ewald time 1.57 (74.62% of Nonbo) +| Nonbond force 2.10 (99.35% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.39% of Force) +| FRC Collect time 0.00 ( 0.14% of Force) +| Other 0.00 ( 0.13% of Force) +| Force time 2.11 (97.43% of Runmd) +| Shake time 0.01 ( 0.24% of Runmd) +| Verlet update time 0.01 ( 0.32% of Runmd) +| CRD distribute time 0.00 ( 0.04% of Runmd) +| Other 0.04 ( 1.97% of Runmd) +| Runmd Time 2.17 (97.15% of Total) +| Other 0.06 ( 2.58% of Total) +| Total time 2.23 (100.0% of ALL ) + +| Number of list builds : 20 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 3.57 Per Step(ms) = 71.43 -| ns/day = 2.42 seconds/ns = 35714.90 +| Elapsed(s) = 2.17 Per Step(ms) = 43.40 +| ns/day = 3.98 seconds/ns = 21701.09 | ----------------------------------------------------- -| Job began at 17:59:34.530 on 06/14/2016 -| Setup done at 17:59:34.592 on 06/14/2016 -| Run done at 17:59:38.163 on 06/14/2016 -| wallclock() was called 3211 times +| Job began at 19:24:35.570 on 09/21/2018 +| Setup done at 19:24:35.635 on 09/21/2018 +| Run done at 19:24:37.804 on 09/21/2018 +| wallclock() was called 3781 times diff --git test/nfe/premd/save/mdout.3.pmemd test/nfe/premd/save/mdout.3.pmemd new file mode 100644 index 0000000000..326b6f7f96 --- /dev/null +++ test/nfe/premd/save/mdout.3.pmemd @@ -0,0 +1,429 @@ + + ------------------------------------------------------- + Amber 18 PMEMD 2018 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 18 + +| Run on 09/21/2018 at 19:25:45 + +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/premd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output + +File Assignments: +| MDIN: mdin.3 +| MDOUT: mdout.3 +| INPCRD: inpcrd.3 +| PARM: prmtop +| RESTRT: restrt.3 +| REFC: refc +| MDVEL: mdvel.002 +| MDEN: mden.002 +| MDCRD: mdcrd.3 +| MDINFO: /dev/null +|LOGFILE: logfile.002 +| MDFRC: mdfrc.002 + + + Here is the input file: + + + &cntrl + igb = 0, ntx = 7, irest = 1, + ntb = 1, ntp = 0, temp0 = 320.0, + ntt = 1, gamma_ln = 0.0, + ntf = 2, ntc = 2, tol = 0.00001, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, + numexchg = 10, infe = 1, + / + + &pmd + output_file = 'pmd.3.txt' + output_freq = 1 + cv_file = 'cv.3' + / + + +| irandom = 1, using AMBER's internal random number generator (default). + + +| Conditional Compilation Defines Used: +| MPI +| PUBFFT +| BINTRAJ +| EMIL + +| Largest sphere to fit in unit cell has radius = 14.075 + +| New format PARM file being parsed. +| Version = 1.000 Date = 09/01/07 Time = 11:29:05 + +| Note: 1-4 EEL scale factors were NOT found in the topology file. +| Using default value of 1.2. + +| Note: 1-4 VDW scale factors were NOT found in the topology file. +| Using default value of 2.0. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 + NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 + NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 + NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 + NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 + IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 6 6 6 +| Direct force subcell size = 5.7460 5.7460 5.7460 + + BOX TYPE: TRUNCATED OCTAHEDRON + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + +NGLY + +General flags: + imin = 0, nmropt = 0 + +Replica exchange + numexchg= 10, rem= 3 + +Nature and format of input: + ntx = 7, irest = 1, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 5, ntrx = 1, ntwr = 50 + iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 2, ntb = 1, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 0 + +Molecular dynamics: + nstlim = 5, nscm = 1000, nrespa = 1 + t = 0.00000, dt = 0.00200, vlimit = 20.00000 + +Berendsen (weak-coupling) temperature regulation: + temp0 = 320.00000, tempi = 0.00000, tautp = 1.00000 + +SHAKE: + ntc = 2, jfastw = 0 + tol = 0.00001 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 5 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 1 + Box X = 34.476 Box Y = 34.476 Box Z = 34.476 + Alpha = 109.471 Beta = 109.471 Gamma = 109.471 + NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + +NGLY + begin time read from input coords = 0.000 ps + + + Number of triangulated 3-point waters found: 1001 + + Sum of charges from parm topology file = -0.00000001 + Forcing neutrality... + +| Dynamic Memory, Types Used: +| Reals 245730 +| Integers 211573 + +| Nonbonded Pairs Initial Allocation: 358302 + +| Running AMBER/MPI version on 2 MPI task + + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + --------------------------------------------------- + APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION + using 5000.0 points per unit in tabled values + TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff +| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 +| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 + --------------------------------------------------- +|--------------------------------------------------- +| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.47 +| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.89 +|--------------------------------------------------- + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + NFE : + NFE : output_file = pmd.3.txt + NFE : output_freq = 1 (0.0020 ps) + NFE : + NFE : CV #1 << anchor : position = 2.000000, 7.000000, 7.000000, 12.000000 + NFE : strength = 3.000000, 3.000000 >> + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + + + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 309.47 PRESS = 0.0 + Etot = -8148.3747 EKtot = 1956.2272 EPtot = -10104.6019 + BOND = 27.8338 ANGLE = 67.0127 DIHED = 74.1063 + 1-4 NB = 29.5980 1-4 EEL = 526.8812 VDWAALS = 1332.7204 + EELEC = -12164.3317 EHBOND = 0.0000 RESTRAINT = 1.5773 + EAMBER (non-restraint) = -10106.1793 + Ewald error estimate: 0.2771E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 1.577 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 318.24 PRESS = 0.0 + Etot = -8057.8055 EKtot = 2011.6624 EPtot = -10069.4678 + BOND = 31.4275 ANGLE = 73.8749 DIHED = 78.6156 + 1-4 NB = 33.3465 1-4 EEL = 533.7908 VDWAALS = 1430.6460 + EELEC = -12251.5089 EHBOND = 0.0000 RESTRAINT = 0.3397 + EAMBER (non-restraint) = -10069.8075 + Ewald error estimate: 0.4813E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.340 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 325.08 PRESS = 0.0 + Etot = -8058.2731 EKtot = 2054.8859 EPtot = -10113.1590 + BOND = 23.6875 ANGLE = 74.1512 DIHED = 73.1603 + 1-4 NB = 32.6120 1-4 EEL = 540.9514 VDWAALS = 1436.6876 + EELEC = -12294.7403 EHBOND = 0.0000 RESTRAINT = 0.3312 + EAMBER (non-restraint) = -10113.4902 + Ewald error estimate: 0.2507E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.331 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 320.24 PRESS = 0.0 + Etot = -8057.7688 EKtot = 2024.3408 EPtot = -10082.1096 + BOND = 31.5904 ANGLE = 76.3049 DIHED = 76.3418 + 1-4 NB = 35.7187 1-4 EEL = 541.8974 VDWAALS = 1427.1453 + EELEC = -12271.4222 EHBOND = 0.0000 RESTRAINT = 0.3141 + EAMBER (non-restraint) = -10082.4238 + Ewald error estimate: 0.1687E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.314 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 317.56 PRESS = 0.0 + Etot = -8057.6238 EKtot = 2007.3881 EPtot = -10065.0119 + BOND = 31.8921 ANGLE = 62.2308 DIHED = 79.9793 + 1-4 NB = 32.7820 1-4 EEL = 541.2369 VDWAALS = 1427.3876 + EELEC = -12240.8164 EHBOND = 0.0000 RESTRAINT = 0.2957 + EAMBER (non-restraint) = -10065.3076 + Ewald error estimate: 0.1090E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.296 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 311.55 PRESS = 0.0 + Etot = -8057.4936 EKtot = 1969.3841 EPtot = -10026.8778 + BOND = 32.6072 ANGLE = 63.3747 DIHED = 83.3507 + 1-4 NB = 35.2471 1-4 EEL = 538.1261 VDWAALS = 1445.3751 + EELEC = -12225.2337 EHBOND = 0.0000 RESTRAINT = 0.2752 + EAMBER (non-restraint) = -10027.1529 + Ewald error estimate: 0.6948E-04 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.275 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 308.98 PRESS = 0.0 + Etot = -8057.3530 EKtot = 1953.1512 EPtot = -10010.5042 + BOND = 31.2338 ANGLE = 63.2499 DIHED = 77.8451 + 1-4 NB = 36.3124 1-4 EEL = 542.0073 VDWAALS = 1437.6859 + EELEC = -12199.0961 EHBOND = 0.0000 RESTRAINT = 0.2575 + EAMBER (non-restraint) = -10010.7617 + Ewald error estimate: 0.3057E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.258 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 304.92 PRESS = 0.0 + Etot = -8056.4911 EKtot = 1927.4777 EPtot = -9983.9688 + BOND = 22.8244 ANGLE = 71.3503 DIHED = 78.0854 + 1-4 NB = 39.4656 1-4 EEL = 536.4455 VDWAALS = 1384.1603 + EELEC = -12116.5424 EHBOND = 0.0000 RESTRAINT = 0.2420 + EAMBER (non-restraint) = -9984.2108 + Ewald error estimate: 0.1498E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.242 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 307.51 PRESS = 0.0 + Etot = -8055.7214 EKtot = 1943.8395 EPtot = -9999.5609 + BOND = 26.0709 ANGLE = 76.0954 DIHED = 77.2167 + 1-4 NB = 39.1124 1-4 EEL = 537.5107 VDWAALS = 1322.3124 + EELEC = -12078.1173 EHBOND = 0.0000 RESTRAINT = 0.2379 + EAMBER (non-restraint) = -9999.7988 + Ewald error estimate: 0.2664E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.238 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 315.45 PRESS = 0.0 + Etot = -8055.7951 EKtot = 1994.0534 EPtot = -10049.8485 + BOND = 24.9537 ANGLE = 67.7324 DIHED = 72.2504 + 1-4 NB = 34.9957 1-4 EEL = 539.6617 VDWAALS = 1296.1682 + EELEC = -12085.8453 EHBOND = 0.0000 RESTRAINT = 0.2346 + EAMBER (non-restraint) = -10050.0832 + Ewald error estimate: 0.3133E-03 + TEMP0 = 320.0000 REPNUM = 3 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.235 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines, Average for All Tasks: +| +| Routine Sec % +| ------------------------------ +| DataDistrib 0.02 1.46 +| Nonbond 1.03 94.51 +| Bond 0.00 0.00 +| Angle 0.00 0.05 +| Dihedral 0.01 0.55 +| Shake 0.01 0.50 +| RunMD 0.02 1.42 +| Other 0.02 1.51 +| ------------------------------ +| Total 1.09 + +| PME Nonbond Pairlist CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.09 +| Build List 0.24 21.68 +| --------------------------------- +| Total 0.24 21.77 + +| PME Direct Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.52 47.62 +| Exclude Masked 0.01 0.55 +| Other 0.01 1.19 +| --------------------------------- +| Total 0.54 49.36 + +| PME Reciprocal Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.02 2.29 +| Grid Charges 0.02 2.01 +| Scalar Sum 0.04 3.71 +| Gradient Sum 0.03 2.74 +| FFT 0.14 12.63 +| --------------------------------- +| Total 0.26 23.38 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 + +| Final Performance Info: +| ----------------------------------------------------- +| Average timings for last 45 steps: +| Elapsed(s) = 0.97 Per Step(ms) = 21.55 +| ns/day = 8.02 seconds/ns = 10774.31 +| +| Average timings for all steps: +| Elapsed(s) = 1.09 Per Step(ms) = 21.88 +| ns/day = 7.90 seconds/ns = 10938.77 +| ----------------------------------------------------- + +| Master Setup CPU time: 0.07 seconds +| Master NonSetup CPU time: 1.09 seconds +| Master Total CPU time: 1.16 seconds 0.00 hours + +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds +| Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/premd/save/mdout.4 test/nfe/premd/save/mdout.4 index 93046877f4..4c892f0486 100644 --- test/nfe/premd/save/mdout.4 +++ test/nfe/premd/save/mdout.4 @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/14/2016 at 17:59:34 +| Run on 09/21/2018 at 19:24:35 -| Executable path: /home/feng/git_feng/amber/bin/sander.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/premd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/premd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -45,9 +45,9 @@ File Assignments: ntb = 1, ntp = 0, temp0 = 330.0, ntt = 1, gamma_ln = 0.0, ntf = 2, ntc = 2, tol = 0.00001, - cut = 8.0, dt = 0.002, + cut = 8.0, dt = 0.002, ig = 71277 ntpr = 5, ntwx = 0, nstlim = 5, - numexchg = 10, infe = 1, + numexchg = 10, infe = 1, / &pmd @@ -83,8 +83,8 @@ File Assignments: | Integer 115557 | Max Pairs 1047666 | nblistReal 37716 -| nblist Int 124375 -| Total 7742 kbytes +| nblist Int 113677 +| Total 7701 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -106,7 +106,7 @@ General flags: imin = 0, nmropt = 0 Replica exchange - numexchg= 10, rem= 1 + numexchg= 10, rem= 3 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 @@ -157,18 +157,35 @@ NGLY Number of triangulated 3-point waters found: 1001 | Atom division among processors: -| 0 3143 +| 0 1571 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... -| Running AMBER/MPI version on 1 nodes +| Running AMBER/MPI version on 2 nodes -| MULTISANDER: 4 groups. 1 processors out of 4 total. +| MULTISANDER: 4 groups. 2 processors out of 8 total. -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + NFE : + NFE : output_file = pmd.4.txt + NFE : output_freq = 1 (0.0020 ps) + NFE : + NFE : CV #1 << anchor : position = 3.000000, 8.000000, 8.000000, 13.000000 + NFE : strength = 4.000000, 4.000000 >> + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + | # of SOLUTE degrees of freedom (RNDFP): 6365. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 6362. NUM_NOSHAKE = 0 CORRECTED RNDFP = 6362. @@ -180,158 +197,203 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 651355 +| Local SIZE OF NONBOND LIST = 321415 | TOTAL SIZE OF NONBOND LIST = 651355 - NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 301.86 PRESS = 0.0 - Etot = -8309.1724 EKtot = 1908.1256 EPtot = -10217.2979 - BOND = 30.1514 ANGLE = 54.3792 DIHED = 72.3485 - 1-4 NB = 28.6253 1-4 EEL = 540.2686 VDWAALS = 1443.5605 - EELEC = -12386.6316 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.4224E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 1 + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 330.40 PRESS = 0.0 + Etot = -7991.5106 EKtot = 2088.5548 EPtot = -10080.0655 + BOND = 22.2909 ANGLE = 65.8081 DIHED = 76.2409 + 1-4 NB = 33.3644 1-4 EEL = 538.2948 VDWAALS = 1420.5312 + EELEC = -12240.9677 EHBOND = 0.0000 RESTRAINT = 4.3718 + EAMBER (non-restraint) = -10084.4372 + Ewald error estimate: 0.9206E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 1 ------------------------------------------------------------------------------ - - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 294.86 PRESS = 0.0 - Etot = -8307.6439 EKtot = 1863.8606 EPtot = -10171.5045 - BOND = 28.7488 ANGLE = 67.6617 DIHED = 84.6855 - 1-4 NB = 29.7461 1-4 EEL = 534.6238 VDWAALS = 1452.3013 - EELEC = -12369.2716 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.3009E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 2 + NFE restraints: SMD : 0.000 PMD : 4.372 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 309.94 PRESS = 0.0 + Etot = -8087.5520 EKtot = 1959.2254 EPtot = -10046.7774 + BOND = 33.8340 ANGLE = 60.0649 DIHED = 77.8574 + 1-4 NB = 31.0830 1-4 EEL = 525.3031 VDWAALS = 1343.1938 + EELEC = -12118.1173 EHBOND = 0.0000 RESTRAINT = 0.0036 + EAMBER (non-restraint) = -10046.7811 + Ewald error estimate: 0.9161E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 2 ------------------------------------------------------------------------------ - - NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 291.94 PRESS = 0.0 - Etot = -8306.6870 EKtot = 1845.4439 EPtot = -10152.1309 - BOND = 30.4611 ANGLE = 64.1200 DIHED = 83.4350 - 1-4 NB = 28.8723 1-4 EEL = 528.4570 VDWAALS = 1467.1623 - EELEC = -12354.6387 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2633E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 3 + NFE restraints: SMD : 0.000 PMD : 0.004 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 312.46 PRESS = 0.0 + Etot = -8087.2982 EKtot = 1975.1519 EPtot = -10062.4501 + BOND = 34.6602 ANGLE = 58.1385 DIHED = 76.6790 + 1-4 NB = 29.2035 1-4 EEL = 520.9408 VDWAALS = 1337.9644 + EELEC = -12120.0447 EHBOND = 0.0000 RESTRAINT = 0.0081 + EAMBER (non-restraint) = -10062.4582 + Ewald error estimate: 0.1071E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 3 ------------------------------------------------------------------------------ - - NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 292.64 PRESS = 0.0 - Etot = -8305.5021 EKtot = 1849.8591 EPtot = -10155.3612 - BOND = 34.1713 ANGLE = 70.0646 DIHED = 78.5036 - 1-4 NB = 30.7533 1-4 EEL = 536.6517 VDWAALS = 1461.3446 - EELEC = -12366.8502 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2740E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 4 + NFE restraints: SMD : 0.000 PMD : 0.008 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 309.16 PRESS = 0.0 + Etot = -8085.5098 EKtot = 1954.2537 EPtot = -10039.7635 + BOND = 28.0158 ANGLE = 63.1628 DIHED = 77.7355 + 1-4 NB = 31.7456 1-4 EEL = 522.3824 VDWAALS = 1318.7538 + EELEC = -12081.5728 EHBOND = 0.0000 RESTRAINT = 0.0134 + EAMBER (non-restraint) = -10039.7769 + Ewald error estimate: 0.9313E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 4 ------------------------------------------------------------------------------ - - NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 299.16 PRESS = 0.0 - Etot = -8305.8009 EKtot = 1891.0388 EPtot = -10196.8397 - BOND = 25.1265 ANGLE = 59.2098 DIHED = 82.5059 - 1-4 NB = 32.5421 1-4 EEL = 537.0157 VDWAALS = 1455.5479 - EELEC = -12388.7876 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1450E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 5 + NFE restraints: SMD : 0.000 PMD : 0.013 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 315.35 PRESS = 0.0 + Etot = -8084.9174 EKtot = 1993.4158 EPtot = -10078.3332 + BOND = 23.2393 ANGLE = 68.9997 DIHED = 73.2534 + 1-4 NB = 30.8071 1-4 EEL = 523.2149 VDWAALS = 1300.9266 + EELEC = -12098.7911 EHBOND = 0.0000 RESTRAINT = 0.0170 + EAMBER (non-restraint) = -10078.3502 + Ewald error estimate: 0.4680E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 5 ------------------------------------------------------------------------------ - - NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 296.58 PRESS = 0.0 - Etot = -8304.6398 EKtot = 1874.7346 EPtot = -10179.3744 - BOND = 26.6963 ANGLE = 57.5245 DIHED = 75.8293 - 1-4 NB = 34.2190 1-4 EEL = 534.2284 VDWAALS = 1449.5239 - EELEC = -12357.3957 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1265E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 6 + NFE restraints: SMD : 0.000 PMD : 0.017 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 311.18 PRESS = 0.0 + Etot = -8083.1000 EKtot = 1967.0370 EPtot = -10050.1370 + BOND = 37.7035 ANGLE = 67.0455 DIHED = 75.6358 + 1-4 NB = 31.4580 1-4 EEL = 515.8378 VDWAALS = 1284.1719 + EELEC = -12062.0091 EHBOND = 0.0000 RESTRAINT = 0.0196 + EAMBER (non-restraint) = -10050.1566 + Ewald error estimate: 0.7892E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 6 ------------------------------------------------------------------------------ - - NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 301.32 PRESS = 0.0 - Etot = -8304.6620 EKtot = 1904.7125 EPtot = -10209.3745 - BOND = 21.5411 ANGLE = 62.9284 DIHED = 79.0721 - 1-4 NB = 33.5371 1-4 EEL = 540.4249 VDWAALS = 1443.7385 - EELEC = -12390.6167 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1115E-03 - TEMP0 = 310.0000 REPNUM = 4 EXCHANGE# = 7 + NFE restraints: SMD : 0.000 PMD : 0.020 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 312.82 PRESS = 0.0 + Etot = -8082.6637 EKtot = 1977.4011 EPtot = -10060.0648 + BOND = 18.5770 ANGLE = 62.1037 DIHED = 80.2639 + 1-4 NB = 31.6286 1-4 EEL = 535.3504 VDWAALS = 1262.4525 + EELEC = -12050.4645 EHBOND = 0.0000 RESTRAINT = 0.0238 + EAMBER (non-restraint) = -10060.0885 + Ewald error estimate: 0.1117E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 7 ------------------------------------------------------------------------------ - - NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 288.00 PRESS = 0.0 - Etot = -8364.7432 EKtot = 1820.5201 EPtot = -10185.2633 - BOND = 29.7770 ANGLE = 51.9370 DIHED = 80.2396 - 1-4 NB = 32.5631 1-4 EEL = 541.2864 VDWAALS = 1440.9650 - EELEC = -12362.0313 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1838E-03 - TEMP0 = 300.0000 REPNUM = 4 EXCHANGE# = 8 + NFE restraints: SMD : 0.000 PMD : 0.024 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 315.81 PRESS = 0.0 + Etot = -8081.6569 EKtot = 1996.2861 EPtot = -10077.9430 + BOND = 24.4979 ANGLE = 61.7163 DIHED = 76.6844 + 1-4 NB = 32.8313 1-4 EEL = 533.8761 VDWAALS = 1250.3083 + EELEC = -12057.8836 EHBOND = 0.0000 RESTRAINT = 0.0263 + EAMBER (non-restraint) = -10077.9693 + Ewald error estimate: 0.7140E-05 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 8 ------------------------------------------------------------------------------ - - NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 293.44 PRESS = 0.0 - Etot = -8364.7592 EKtot = 1854.9274 EPtot = -10219.6866 - BOND = 27.9142 ANGLE = 55.4647 DIHED = 77.0995 - 1-4 NB = 33.2218 1-4 EEL = 543.3219 VDWAALS = 1453.4622 - EELEC = -12410.1709 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.1935E-03 - TEMP0 = 300.0000 REPNUM = 4 EXCHANGE# = 9 + NFE restraints: SMD : 0.000 PMD : 0.026 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 313.55 PRESS = 0.0 + Etot = -8080.4606 EKtot = 1982.0558 EPtot = -10062.5164 + BOND = 34.3628 ANGLE = 67.9599 DIHED = 71.2922 + 1-4 NB = 29.6434 1-4 EEL = 529.4174 VDWAALS = 1267.9895 + EELEC = -12063.2131 EHBOND = 0.0000 RESTRAINT = 0.0316 + EAMBER (non-restraint) = -10062.5480 + Ewald error estimate: 0.9983E-05 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 9 ------------------------------------------------------------------------------ - - NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 286.04 PRESS = 0.0 - Etot = -8363.1412 EKtot = 1808.1261 EPtot = -10171.2673 - BOND = 32.9138 ANGLE = 63.4880 DIHED = 76.9674 - 1-4 NB = 35.1625 1-4 EEL = 540.2692 VDWAALS = 1475.6307 - EELEC = -12395.6989 EHBOND = 0.0000 RESTRAINT = 0.0000 - Ewald error estimate: 0.2557E-03 - TEMP0 = 300.0000 REPNUM = 4 EXCHANGE# = 10 + NFE restraints: SMD : 0.000 PMD : 0.032 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 311.24 PRESS = 0.0 + Etot = -8079.0669 EKtot = 1967.4255 EPtot = -10046.4924 + BOND = 27.6493 ANGLE = 64.1284 DIHED = 77.3008 + 1-4 NB = 34.0459 1-4 EEL = 542.0740 VDWAALS = 1311.6370 + EELEC = -12103.3588 EHBOND = 0.0000 RESTRAINT = 0.0309 + EAMBER (non-restraint) = -10046.5234 + Ewald error estimate: 0.1760E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 10 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.000 PMD : 0.031 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.30% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.01 ( 0.27% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.30 (91.25% of List ) -| Other 0.03 ( 8.75% of List ) -| List time 0.33 ( 9.86% of Nonbo) -| Short_ene time 2.26 (99.15% of Direc) -| Other 0.02 ( 0.85% of Direc) -| Direct Ewald time 2.28 (76.59% of Ewald) -| Adjust Ewald time 0.02 ( 0.62% of Ewald) +| Build the list 0.48 (95.72% of List ) +| Other 0.02 ( 4.28% of List ) +| List time 0.51 (24.21% of Nonbo) +| Short_ene time 1.00 (97.89% of Direc) +| Other 0.02 ( 2.11% of Direc) +| Direct Ewald time 1.02 (64.60% of Ewald) +| Adjust Ewald time 0.01 ( 0.47% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.03 ( 4.05% of Recip) -| Fill charge grid 0.05 ( 7.35% of Recip) -| Scalar sum 0.28 (41.09% of Recip) -| Grad sum 0.11 (16.29% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.21 (100.0% of FFT t) -| FFT time 0.21 (31.18% of Recip) -| Other 0.00 ( 0.04% of Recip) -| Recip Ewald time 0.67 (22.62% of Ewald) -| Force Adjust 0.00 ( 0.03% of Ewald) -| Virial junk 0.00 ( 0.06% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 2.98 (90.14% of Nonbo) -| Nonbond force 3.30 (99.42% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.47% of Force) -| Other 0.00 ( 0.11% of Force) -| Force time 3.32 (91.73% of Runmd) -| Shake time 0.02 ( 0.46% of Runmd) -| Verlet update time 0.01 ( 0.37% of Runmd) -| Other 0.27 ( 7.44% of Runmd) -| Runmd Time 3.62 (98.34% of Total) -| Other 0.05 ( 1.35% of Total) -| Total time 3.68 (100.0% of ALL ) - -| Highest rstack allocated: 191619 -| Highest istack allocated: 3143 +| Fill Bspline coeffs 0.02 ( 5.94% of Recip) +| Fill charge grid 0.03 ( 6.61% of Recip) +| Scalar sum 0.11 (26.18% of Recip) +| Grad sum 0.06 (14.99% of Recip) +| FFT back comm time 0.01 ( 7.84% of FFT t) +| Other 0.15 (92.16% of FFT t) +| FFT time 0.17 (41.16% of Recip) +| Other 0.02 ( 5.12% of Recip) +| Recip Ewald time 0.40 (25.55% of Ewald) +| Force Adjust 0.15 ( 9.19% of Ewald) +| Virial junk 0.00 ( 0.13% of Ewald) +| Other 0.00 ( 0.06% of Ewald) +| Ewald time 1.58 (75.78% of Nonbo) +| Nonbond force 2.09 (99.36% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.35% of Force) +| FRC Collect time 0.00 ( 0.12% of Force) +| Other 0.00 ( 0.17% of Force) +| Force time 2.10 (96.93% of Runmd) +| Shake time 0.00 ( 0.22% of Runmd) +| Verlet update time 0.01 ( 0.34% of Runmd) +| CRD distribute time 0.00 ( 0.04% of Runmd) +| Other 0.05 ( 2.47% of Runmd) +| Runmd Time 2.17 (97.14% of Total) +| Other 0.06 ( 2.58% of Total) +| Total time 2.23 (100.0% of ALL ) + +| Number of list builds : 19 + +| Highest rstack allocated: 146106 +| Highest istack allocated: 2444 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 3.62 Per Step(ms) = 72.44 -| ns/day = 2.39 seconds/ns = 36222.36 +| Elapsed(s) = 2.17 Per Step(ms) = 43.39 +| ns/day = 3.98 seconds/ns = 21694.07 | ----------------------------------------------------- -| Job began at 17:59:34.530 on 06/14/2016 -| Setup done at 17:59:34.592 on 06/14/2016 -| Run done at 17:59:38.214 on 06/14/2016 -| wallclock() was called 3211 times +| Job began at 19:24:35.570 on 09/21/2018 +| Setup done at 19:24:35.635 on 09/21/2018 +| Run done at 19:24:37.804 on 09/21/2018 +| wallclock() was called 3779 times diff --git test/nfe/premd/save/mdout.4.pmemd test/nfe/premd/save/mdout.4.pmemd new file mode 100644 index 0000000000..e755a3f701 --- /dev/null +++ test/nfe/premd/save/mdout.4.pmemd @@ -0,0 +1,429 @@ + + ------------------------------------------------------- + Amber 18 PMEMD 2018 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 18 + +| Run on 09/21/2018 at 19:25:45 + +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/premd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output + +File Assignments: +| MDIN: mdin.4 +| MDOUT: mdout.4 +| INPCRD: inpcrd.4 +| PARM: prmtop +| RESTRT: restrt.4 +| REFC: refc +| MDVEL: mdvel.003 +| MDEN: mden.003 +| MDCRD: mdcrd.4 +| MDINFO: /dev/null +|LOGFILE: logfile.003 +| MDFRC: mdfrc.003 + + + Here is the input file: + + + &cntrl + igb = 0, ntx = 7, irest = 1, + ntb = 1, ntp = 0, temp0 = 330.0, + ntt = 1, gamma_ln = 0.0, + ntf = 2, ntc = 2, tol = 0.00001, + cut = 8.0, dt = 0.002, ig = 71277 + ntpr = 5, ntwx = 0, nstlim = 5, + numexchg = 10, infe = 1, + / + + &pmd + output_file = 'pmd.4.txt' + output_freq = 1 + cv_file = 'cv.4' + / + + +| irandom = 1, using AMBER's internal random number generator (default). + + +| Conditional Compilation Defines Used: +| MPI +| PUBFFT +| BINTRAJ +| EMIL + +| Largest sphere to fit in unit cell has radius = 14.075 + +| New format PARM file being parsed. +| Version = 1.000 Date = 09/01/07 Time = 11:29:05 + +| Note: 1-4 EEL scale factors were NOT found in the topology file. +| Using default value of 1.2. + +| Note: 1-4 VDW scale factors were NOT found in the topology file. +| Using default value of 2.0. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 + NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 + NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 + NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 + NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 + IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 6 6 6 +| Direct force subcell size = 5.7460 5.7460 5.7460 + + BOX TYPE: TRUNCATED OCTAHEDRON + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + +NGLY + +General flags: + imin = 0, nmropt = 0 + +Replica exchange + numexchg= 10, rem= 3 + +Nature and format of input: + ntx = 7, irest = 1, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 5, ntrx = 1, ntwr = 50 + iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 2, ntb = 1, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 0 + +Molecular dynamics: + nstlim = 5, nscm = 1000, nrespa = 1 + t = 0.00000, dt = 0.00200, vlimit = 20.00000 + +Berendsen (weak-coupling) temperature regulation: + temp0 = 330.00000, tempi = 0.00000, tautp = 1.00000 + +SHAKE: + ntc = 2, jfastw = 0 + tol = 0.00001 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 5 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 1 + Box X = 34.476 Box Y = 34.476 Box Z = 34.476 + Alpha = 109.471 Beta = 109.471 Gamma = 109.471 + NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + +NGLY + begin time read from input coords = 0.000 ps + + + Number of triangulated 3-point waters found: 1001 + + Sum of charges from parm topology file = -0.00000001 + Forcing neutrality... + +| Dynamic Memory, Types Used: +| Reals 245716 +| Integers 210016 + +| Nonbonded Pairs Initial Allocation: 358302 + +| Running AMBER/MPI version on 2 MPI task + + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + --------------------------------------------------- + APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION + using 5000.0 points per unit in tabled values + TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff +| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 +| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 + --------------------------------------------------- +|--------------------------------------------------- +| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.47 +| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION +| with 50.0 points per unit in tabled values +| Relative Error Limit not exceeded for r .gt. 2.89 +|--------------------------------------------------- + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + NFE : + NFE : output_file = pmd.4.txt + NFE : output_freq = 1 (0.0020 ps) + NFE : + NFE : CV #1 << anchor : position = 3.000000, 8.000000, 8.000000, 13.000000 + NFE : strength = 4.000000, 4.000000 >> + NFE : type = 'R_OF_GYRATION' + NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], + NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], + NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], + NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], + NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], + NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) + NFE : + NFE : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ + + + NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 330.40 PRESS = 0.0 + Etot = -7991.5106 EKtot = 2088.5548 EPtot = -10080.0655 + BOND = 22.2909 ANGLE = 65.8081 DIHED = 76.2409 + 1-4 NB = 33.3644 1-4 EEL = 538.2948 VDWAALS = 1420.5312 + EELEC = -12240.9677 EHBOND = 0.0000 RESTRAINT = 4.3718 + EAMBER (non-restraint) = -10084.4372 + Ewald error estimate: 0.9206E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 4.372 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 309.94 PRESS = 0.0 + Etot = -8087.5520 EKtot = 1959.2254 EPtot = -10046.7774 + BOND = 33.8340 ANGLE = 60.0649 DIHED = 77.8574 + 1-4 NB = 31.0830 1-4 EEL = 525.3031 VDWAALS = 1343.1938 + EELEC = -12118.1173 EHBOND = 0.0000 RESTRAINT = 0.0036 + EAMBER (non-restraint) = -10046.7811 + Ewald error estimate: 0.9161E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.004 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 312.46 PRESS = 0.0 + Etot = -8087.2982 EKtot = 1975.1519 EPtot = -10062.4501 + BOND = 34.6602 ANGLE = 58.1385 DIHED = 76.6790 + 1-4 NB = 29.2035 1-4 EEL = 520.9408 VDWAALS = 1337.9644 + EELEC = -12120.0447 EHBOND = 0.0000 RESTRAINT = 0.0081 + EAMBER (non-restraint) = -10062.4582 + Ewald error estimate: 0.1071E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.008 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 309.16 PRESS = 0.0 + Etot = -8085.5098 EKtot = 1954.2537 EPtot = -10039.7635 + BOND = 28.0158 ANGLE = 63.1628 DIHED = 77.7355 + 1-4 NB = 31.7456 1-4 EEL = 522.3824 VDWAALS = 1318.7538 + EELEC = -12081.5728 EHBOND = 0.0000 RESTRAINT = 0.0134 + EAMBER (non-restraint) = -10039.7769 + Ewald error estimate: 0.9313E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.013 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 315.35 PRESS = 0.0 + Etot = -8084.9174 EKtot = 1993.4158 EPtot = -10078.3332 + BOND = 23.2393 ANGLE = 68.9997 DIHED = 73.2534 + 1-4 NB = 30.8071 1-4 EEL = 523.2149 VDWAALS = 1300.9266 + EELEC = -12098.7911 EHBOND = 0.0000 RESTRAINT = 0.0170 + EAMBER (non-restraint) = -10078.3502 + Ewald error estimate: 0.4680E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.017 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 311.18 PRESS = 0.0 + Etot = -8083.1000 EKtot = 1967.0370 EPtot = -10050.1370 + BOND = 37.7035 ANGLE = 67.0455 DIHED = 75.6358 + 1-4 NB = 31.4580 1-4 EEL = 515.8378 VDWAALS = 1284.1719 + EELEC = -12062.0091 EHBOND = 0.0000 RESTRAINT = 0.0196 + EAMBER (non-restraint) = -10050.1566 + Ewald error estimate: 0.7892E-04 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.020 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 312.82 PRESS = 0.0 + Etot = -8082.6637 EKtot = 1977.4011 EPtot = -10060.0648 + BOND = 18.5770 ANGLE = 62.1037 DIHED = 80.2639 + 1-4 NB = 31.6286 1-4 EEL = 535.3504 VDWAALS = 1262.4525 + EELEC = -12050.4645 EHBOND = 0.0000 RESTRAINT = 0.0238 + EAMBER (non-restraint) = -10060.0885 + Ewald error estimate: 0.1117E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.024 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 315.81 PRESS = 0.0 + Etot = -8081.6569 EKtot = 1996.2861 EPtot = -10077.9430 + BOND = 24.4979 ANGLE = 61.7163 DIHED = 76.6844 + 1-4 NB = 32.8313 1-4 EEL = 533.8761 VDWAALS = 1250.3083 + EELEC = -12057.8836 EHBOND = 0.0000 RESTRAINT = 0.0263 + EAMBER (non-restraint) = -10077.9693 + Ewald error estimate: 0.7140E-05 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.026 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 313.55 PRESS = 0.0 + Etot = -8080.4606 EKtot = 1982.0558 EPtot = -10062.5164 + BOND = 34.3628 ANGLE = 67.9599 DIHED = 71.2922 + 1-4 NB = 29.6434 1-4 EEL = 529.4174 VDWAALS = 1267.9895 + EELEC = -12063.2131 EHBOND = 0.0000 RESTRAINT = 0.0316 + EAMBER (non-restraint) = -10062.5480 + Ewald error estimate: 0.9983E-05 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.032 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== + + NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 311.24 PRESS = 0.0 + Etot = -8079.0669 EKtot = 1967.4255 EPtot = -10046.4924 + BOND = 27.6493 ANGLE = 64.1284 DIHED = 77.3008 + 1-4 NB = 34.0459 1-4 EEL = 542.0740 VDWAALS = 1311.6370 + EELEC = -12103.3588 EHBOND = 0.0000 RESTRAINT = 0.0309 + EAMBER (non-restraint) = -10046.5234 + Ewald error estimate: 0.1760E-03 + TEMP0 = 330.0000 REPNUM = 4 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + NFE restraints: SMD : 0.000 PMD : 0.031 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines, Average for All Tasks: +| +| Routine Sec % +| ------------------------------ +| DataDistrib 0.02 1.60 +| Nonbond 1.02 93.73 +| Bond 0.00 0.05 +| Angle 0.00 0.00 +| Dihedral 0.01 0.50 +| Shake 0.00 0.23 +| RunMD 0.01 1.28 +| Other 0.03 2.61 +| ------------------------------ +| Total 1.09 + +| PME Nonbond Pairlist CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.09 +| Build List 0.22 20.32 +| --------------------------------- +| Total 0.22 20.41 + +| PME Direct Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.53 48.56 +| Exclude Masked 0.01 0.69 +| Other 0.02 1.65 +| --------------------------------- +| Total 0.56 50.89 + +| PME Reciprocal Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.02 1.92 +| Grid Charges 0.02 1.42 +| Scalar Sum 0.04 3.89 +| Gradient Sum 0.02 2.29 +| FFT 0.14 12.91 +| --------------------------------- +| Total 0.24 22.43 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 + +| Final Performance Info: +| ----------------------------------------------------- +| Average timings for last 45 steps: +| Elapsed(s) = 0.98 Per Step(ms) = 21.82 +| ns/day = 7.92 seconds/ns = 10908.67 +| +| Average timings for all steps: +| Elapsed(s) = 1.09 Per Step(ms) = 21.88 +| ns/day = 7.90 seconds/ns = 10939.20 +| ----------------------------------------------------- + +| Master Setup CPU time: 0.07 seconds +| Master NonSetup CPU time: 1.09 seconds +| Master Total CPU time: 1.16 seconds 0.00 hours + +| Master Setup wall time: 0 seconds +| Master NonSetup wall time: 1 seconds +| Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/premd/save/pmd.1.txt test/nfe/premd/save/pmd.1.txt index 5b26b596ac..a473062ee6 100644 --- test/nfe/premd/save/pmd.1.txt +++ test/nfe/premd/save/pmd.1.txt @@ -1,66 +1,56 @@ # = NFE%PMD ================================================================== -# << anchor(1) : position = 0.000000,5.000000, 5.000000, 10.000000 +# << anchor(1) : position = 0.000000, 5.000000, 5.000000, 10.000000 # strength = 1.000000, 1.000000 >> # ----------------------------------------------------------------------------- # MD time (ps), CV(1:1) # ============================================================================= - 0.0000 7.36510050 - 0.0020 7.36400128 - 0.0040 7.36293646 - 0.0060 7.36177740 - 0.0080 7.36041800 - 0.0100 7.35882268 - 0.0100 7.35882268 - 0.0120 7.35703354 - 0.0140 7.35513676 - 0.0160 7.35321913 - 0.0180 7.35134756 - 0.0200 7.34956760 - 0.0200 7.34956760 - 0.0220 7.34789487 - 0.0240 7.34630406 - 0.0260 7.34473737 - 0.0280 7.34312980 - 0.0300 7.34142878 - 0.0300 7.34142878 - 0.0320 7.33959460 - 0.0340 7.33758939 - 0.0360 7.33537197 - 0.0380 7.33290649 - 0.0400 7.33018065 - 0.0400 7.33018065 - 0.0420 7.32721594 - 0.0440 7.32405524 - 0.0460 7.32073593 - 0.0480 7.31727508 - 0.0500 7.31367970 - 0.0500 7.31367970 - 0.0520 7.30996834 - 0.0540 7.30618360 - 0.0560 7.30238534 - 0.0580 7.29863124 - 0.0600 7.29496943 - 0.0600 7.29496943 - 0.0620 7.29145643 - 0.0640 7.28816808 - 0.0660 7.28516063 - 0.0680 7.28241255 - 0.0700 7.27982474 - 0.0700 6.27261567 - 0.0720 6.27000993 - 0.0740 6.26767502 - 0.0760 6.26584573 - 0.0780 6.26463044 - 0.0800 6.26397069 - 0.0800 6.26397069 - 0.0820 6.26367644 - 0.0840 6.26352295 - 0.0860 6.26335255 - 0.0880 6.26313422 - 0.0900 6.26296556 - 0.0900 6.26296556 - 0.0920 6.26302343 - 0.0940 6.26347586 - 0.0960 6.26439228 - 0.0980 6.26570991 - 0.1000 6.26727723 + 0.0000 6.30432743 + 0.0020 6.30515884 + 0.0040 6.30596058 + 0.0060 6.30648122 + 0.0080 6.30653688 + 0.0100 7.35880094 + 0.0120 7.35703068 + 0.0140 7.35515232 + 0.0160 7.35325359 + 0.0180 7.35140187 + 0.0200 7.34964220 + 0.0220 7.34798953 + 0.0240 7.34641838 + 0.0260 7.34487115 + 0.0280 7.34328262 + 0.0300 7.34159933 + 0.0320 7.33978046 + 0.0340 7.33778759 + 0.0360 7.33557997 + 0.0380 7.33312314 + 0.0400 7.33040645 + 0.0420 7.32745281 + 0.0440 7.32430600 + 0.0460 7.32100391 + 0.0480 7.31756389 + 0.0500 6.29034087 + 0.0520 6.28898506 + 0.0540 6.28761636 + 0.0560 6.28632411 + 0.0580 6.28511264 + 0.0600 6.28389260 + 0.0620 6.28251996 + 0.0640 6.28085854 + 0.0660 6.27883580 + 0.0680 6.27647387 + 0.0700 6.27390133 + 0.0720 6.27134188 + 0.0740 6.26906235 + 0.0760 6.26728712 + 0.0780 6.26611539 + 0.0800 6.26548288 + 0.0820 6.26519774 + 0.0840 6.26503704 + 0.0860 6.26484659 + 0.0880 6.26459838 + 0.0900 7.25962116 + 0.0920 7.25813382 + 0.0940 7.25638855 + 0.0960 7.25442538 + 0.0980 7.25237868 diff --git test/nfe/premd/save/pmd.1.txt.pmemd test/nfe/premd/save/pmd.1.txt.pmemd new file mode 100644 index 0000000000..1ad8cf1248 --- /dev/null +++ test/nfe/premd/save/pmd.1.txt.pmemd @@ -0,0 +1,56 @@ +# = NFE%PMD ================================================================== +# << anchor(1) : position = 0.000000, 5.000000, 5.000000, 10.000000 +# strength = 1.000000, 1.000000 >> +# ----------------------------------------------------------------------------- +# MD time (ps), CV(1:1) +# ============================================================================= + 0.0000 6.51868743 + 0.0020 6.30515884 + 0.0040 6.30596058 + 0.0060 6.30648122 + 0.0080 6.30653688 + 0.0100 6.30611396 + 0.0120 7.35703068 + 0.0140 7.35515232 + 0.0160 7.35325359 + 0.0180 7.35140187 + 0.0200 7.34964220 + 0.0220 7.34798953 + 0.0240 7.34641838 + 0.0260 7.34487115 + 0.0280 7.34328262 + 0.0300 7.34159933 + 0.0320 7.33978046 + 0.0340 7.33778759 + 0.0360 7.33557997 + 0.0380 7.33312314 + 0.0400 7.33040645 + 0.0420 7.32745281 + 0.0440 7.32430600 + 0.0460 7.32100391 + 0.0480 7.31756389 + 0.0500 7.31399311 + 0.0520 6.28898506 + 0.0540 6.28761636 + 0.0560 6.28632411 + 0.0580 6.28511264 + 0.0600 6.28389260 + 0.0620 6.28251996 + 0.0640 6.28085854 + 0.0660 6.27883580 + 0.0680 6.27647387 + 0.0700 6.27390133 + 0.0720 6.27134188 + 0.0740 6.26906235 + 0.0760 6.26728712 + 0.0780 6.26611539 + 0.0800 6.26548288 + 0.0820 6.26519774 + 0.0840 6.26503704 + 0.0860 6.26484659 + 0.0880 6.26459838 + 0.0900 6.26439116 + 0.0920 7.25813382 + 0.0940 7.25638855 + 0.0960 7.25442538 + 0.0980 7.25237868 diff --git test/nfe/premd/save/pmd.2.txt test/nfe/premd/save/pmd.2.txt index b2ec6aedfe..8115181f75 100644 --- test/nfe/premd/save/pmd.2.txt +++ test/nfe/premd/save/pmd.2.txt @@ -1,66 +1,56 @@ # = NFE%PMD ================================================================== -# << anchor(1) : position = 1.000000,6.000000, 6.000000, 11.000000 +# << anchor(1) : position = 1.000000, 6.000000, 6.000000, 11.000000 # strength = 2.000000, 2.000000 >> # ----------------------------------------------------------------------------- # MD time (ps), CV(1:1) # ============================================================================= - 0.0000 6.30432743 - 0.0020 6.30519743 - 0.0040 6.30603668 - 0.0060 6.30658370 - 0.0080 6.30664969 - 0.0100 6.30622466 - 0.0100 6.30622466 - 0.0120 6.30548311 - 0.0140 6.30467365 - 0.0160 6.30399669 - 0.0180 6.30356081 - 0.0200 6.30339048 - 0.0200 6.30339048 - 0.0220 6.30342095 - 0.0240 6.30348526 - 0.0260 6.30335033 - 0.0280 6.30281643 - 0.0300 6.30181990 - 0.0300 6.30181990 - 0.0320 6.30046100 - 0.0340 6.29893869 - 0.0360 6.29744756 - 0.0380 6.29610677 - 0.0400 6.29494793 - 0.0400 6.29494793 - 0.0420 6.29393610 - 0.0440 6.29298901 - 0.0460 6.29199343 - 0.0480 6.29084689 - 0.0500 6.28951803 - 0.0500 6.28951803 - 0.0520 6.28807269 - 0.0540 6.28663129 - 0.0560 6.28528651 - 0.0580 6.28404184 - 0.0600 6.28280274 - 0.0600 6.28280274 - 0.0620 6.28141588 - 0.0640 6.27973429 - 0.0660 6.27767674 - 0.0680 6.27526084 - 0.0700 6.27261567 - 0.0700 7.27982474 - 0.0720 7.27723835 - 0.0740 7.27462754 - 0.0760 7.27200626 - 0.0780 7.26946364 - 0.0800 7.26712035 - 0.0800 7.26712035 - 0.0820 7.26507476 - 0.0840 7.26335877 - 0.0860 7.26191551 - 0.0880 7.26061006 - 0.0900 7.25926946 - 0.0900 7.25926946 - 0.0920 7.25773935 - 0.0940 7.25594262 - 0.0960 7.25391865 - 0.0980 7.25180493 - 0.1000 7.24976111 + 0.0000 7.36510050 + 0.0020 7.36399971 + 0.0040 7.36293178 + 0.0060 7.36176822 + 0.0080 7.36040308 + 0.0100 6.30611396 + 0.0120 6.30537516 + 0.0140 6.30456989 + 0.0160 6.30389501 + 0.0180 6.30345883 + 0.0200 6.30328756 + 0.0220 6.30331959 + 0.0240 6.30339236 + 0.0260 6.30327779 + 0.0280 6.30278026 + 0.0300 6.30183743 + 0.0320 6.30054726 + 0.0340 6.29910378 + 0.0360 6.29769617 + 0.0380 6.29643979 + 0.0400 6.29536444 + 0.0420 6.29443485 + 0.0440 6.29356912 + 0.0460 6.29265489 + 0.0480 6.29158994 + 0.0500 7.31399311 + 0.0520 7.31025079 + 0.0540 7.30643872 + 0.0560 7.30261626 + 0.0580 7.29884058 + 0.0600 7.29515949 + 0.0620 7.29162951 + 0.0640 7.28832654 + 0.0660 7.28530657 + 0.0680 7.28254735 + 0.0700 7.27994881 + 0.0720 7.27739442 + 0.0740 7.27481568 + 0.0760 7.27222585 + 0.0780 7.26971248 + 0.0800 7.26739445 + 0.0820 7.26536913 + 0.0840 7.26366878 + 0.0860 7.26223840 + 0.0880 7.26094589 + 0.0900 6.26439116 + 0.0920 6.26440213 + 0.0940 6.26480434 + 0.0960 6.26566769 + 0.0980 6.26693037 diff --git test/nfe/premd/save/pmd.2.txt.pmemd test/nfe/premd/save/pmd.2.txt.pmemd new file mode 100644 index 0000000000..63ab9f4e0b --- /dev/null +++ test/nfe/premd/save/pmd.2.txt.pmemd @@ -0,0 +1,56 @@ +# = NFE%PMD ================================================================== +# << anchor(1) : position = 1.000000, 6.000000, 6.000000, 11.000000 +# strength = 2.000000, 2.000000 >> +# ----------------------------------------------------------------------------- +# MD time (ps), CV(1:1) +# ============================================================================= + 0.0000 7.36510050 + 0.0020 7.36399971 + 0.0040 7.36293178 + 0.0060 7.36176822 + 0.0080 7.36040308 + 0.0100 7.35880094 + 0.0120 6.30537516 + 0.0140 6.30456989 + 0.0160 6.30389501 + 0.0180 6.30345883 + 0.0200 6.30328756 + 0.0220 6.30331959 + 0.0240 6.30339236 + 0.0260 6.30327779 + 0.0280 6.30278026 + 0.0300 6.30183743 + 0.0320 6.30054726 + 0.0340 6.29910378 + 0.0360 6.29769617 + 0.0380 6.29643979 + 0.0400 6.29536444 + 0.0420 6.29443485 + 0.0440 6.29356912 + 0.0460 6.29265489 + 0.0480 6.29158994 + 0.0500 6.29034087 + 0.0520 7.31025079 + 0.0540 7.30643872 + 0.0560 7.30261626 + 0.0580 7.29884058 + 0.0600 7.29515949 + 0.0620 7.29162951 + 0.0640 7.28832654 + 0.0660 7.28530657 + 0.0680 7.28254735 + 0.0700 7.27994881 + 0.0720 7.27739442 + 0.0740 7.27481568 + 0.0760 7.27222585 + 0.0780 7.26971248 + 0.0800 7.26739445 + 0.0820 7.26536913 + 0.0840 7.26366878 + 0.0860 7.26223840 + 0.0880 7.26094589 + 0.0900 7.25962116 + 0.0920 6.26440213 + 0.0940 6.26480434 + 0.0960 6.26566769 + 0.0980 6.26693037 diff --git test/nfe/premd/save/pmd.3.txt test/nfe/premd/save/pmd.3.txt index 0f3a16cf6c..3911ba614e 100644 --- test/nfe/premd/save/pmd.3.txt +++ test/nfe/premd/save/pmd.3.txt @@ -1,66 +1,56 @@ # = NFE%PMD ================================================================== -# << anchor(1) : position = 2.000000,7.000000, 7.000000, 12.000000 +# << anchor(1) : position = 2.000000, 7.000000, 7.000000, 12.000000 # strength = 3.000000, 3.000000 >> # ----------------------------------------------------------------------------- # MD time (ps), CV(1:1) # ============================================================================= - 0.0000 6.51868743 - 0.0020 6.51885033 - 0.0040 6.51949635 - 0.0060 6.52042723 - 0.0080 6.52140578 - 0.0100 6.52223467 - 0.0100 6.52223467 - 0.0120 6.52281786 - 0.0140 6.52317455 - 0.0160 6.52340453 - 0.0180 6.52365031 - 0.0200 6.52406835 - 0.0200 6.52406835 - 0.0220 6.52479067 - 0.0240 6.52588975 - 0.0260 6.52737039 - 0.0280 6.52918835 - 0.0300 6.53127909 - 0.0300 6.53127909 - 0.0320 6.53358009 - 0.0340 6.53603984 - 0.0360 6.53861127 - 0.0380 6.54124012 - 0.0400 6.54387134 - 0.0400 6.54387134 - 0.0420 6.54647710 - 0.0440 6.54907647 - 0.0460 6.55172406 - 0.0480 6.55447932 - 0.0500 6.55737793 - 0.0500 6.55737793 - 0.0520 6.56041807 - 0.0540 6.56356098 - 0.0560 6.56673809 - 0.0580 6.56986291 - 0.0600 6.57285591 - 0.0600 6.57285591 - 0.0620 6.57567949 - 0.0640 6.57836766 - 0.0660 6.58102557 - 0.0680 6.58377189 - 0.0700 6.58664915 - 0.0700 6.58664915 - 0.0720 6.58957378 - 0.0740 6.59235784 - 0.0760 6.59477998 - 0.0780 6.59666827 - 0.0800 6.59796362 - 0.0800 6.59796362 - 0.0820 6.59873962 - 0.0840 6.59917495 - 0.0860 6.59949902 - 0.0880 6.59992599 - 0.0900 6.60057641 - 0.0900 6.60057641 - 0.0920 6.60140996 - 0.0940 6.60222080 - 0.0960 6.60271761 - 0.0980 6.60265202 - 0.1000 6.60193569 + 0.0000 8.01434902 + 0.0020 8.01662131 + 0.0040 8.01917278 + 0.0060 8.02212654 + 0.0080 8.02545614 + 0.0100 6.52243073 + 0.0120 6.52307292 + 0.0140 6.52349165 + 0.0160 6.52379053 + 0.0180 6.52411430 + 0.0200 6.52461906 + 0.0220 6.52543331 + 0.0240 6.52662371 + 0.0260 6.52818857 + 0.0280 6.53007895 + 0.0300 6.53222893 + 0.0320 6.53457842 + 0.0340 6.53708084 + 0.0360 6.53969477 + 0.0380 6.54237036 + 0.0400 6.54505569 + 0.0420 6.54772527 + 0.0440 6.55039913 + 0.0460 6.55312988 + 0.0480 6.55597160 + 0.0500 6.55895319 + 0.0520 6.56206782 + 0.0540 6.56527550 + 0.0560 6.56850917 + 0.0580 6.57168324 + 0.0600 6.57471677 + 0.0620 6.57756880 + 0.0640 6.58027002 + 0.0660 6.58292329 + 0.0680 6.58564644 + 0.0700 6.58848343 + 0.0720 6.59135621 + 0.0740 6.59408679 + 0.0760 6.59646553 + 0.0780 6.59832967 + 0.0800 6.59962372 + 0.0820 6.60041873 + 0.0840 6.60088649 + 0.0860 6.60124892 + 0.0880 6.60171471 + 0.0900 6.60240093 + 0.0920 6.60326349 + 0.0940 6.60409211 + 0.0960 6.60459170 + 0.0980 6.60451197 diff --git test/nfe/premd/save/pmd.3.txt.pmemd test/nfe/premd/save/pmd.3.txt.pmemd new file mode 100644 index 0000000000..a9ecf21c04 --- /dev/null +++ test/nfe/premd/save/pmd.3.txt.pmemd @@ -0,0 +1,56 @@ +# = NFE%PMD ================================================================== +# << anchor(1) : position = 2.000000, 7.000000, 7.000000, 12.000000 +# strength = 3.000000, 3.000000 >> +# ----------------------------------------------------------------------------- +# MD time (ps), CV(1:1) +# ============================================================================= + 0.0000 8.01434902 + 0.0020 8.01662131 + 0.0040 8.01917278 + 0.0060 8.02212654 + 0.0080 8.02545614 + 0.0100 8.02900483 + 0.0120 6.52307292 + 0.0140 6.52349165 + 0.0160 6.52379053 + 0.0180 6.52411430 + 0.0200 6.52461906 + 0.0220 6.52543331 + 0.0240 6.52662371 + 0.0260 6.52818857 + 0.0280 6.53007895 + 0.0300 6.53222893 + 0.0320 6.53457842 + 0.0340 6.53708084 + 0.0360 6.53969477 + 0.0380 6.54237036 + 0.0400 6.54505569 + 0.0420 6.54772527 + 0.0440 6.55039913 + 0.0460 6.55312988 + 0.0480 6.55597160 + 0.0500 6.55895319 + 0.0520 6.56206782 + 0.0540 6.56527550 + 0.0560 6.56850917 + 0.0580 6.57168324 + 0.0600 6.57471677 + 0.0620 6.57756880 + 0.0640 6.58027002 + 0.0660 6.58292329 + 0.0680 6.58564644 + 0.0700 6.58848343 + 0.0720 6.59135621 + 0.0740 6.59408679 + 0.0760 6.59646553 + 0.0780 6.59832967 + 0.0800 6.59962372 + 0.0820 6.60041873 + 0.0840 6.60088649 + 0.0860 6.60124892 + 0.0880 6.60171471 + 0.0900 6.60240093 + 0.0920 6.60326349 + 0.0940 6.60409211 + 0.0960 6.60459170 + 0.0980 6.60451197 diff --git test/nfe/premd/save/pmd.4.txt test/nfe/premd/save/pmd.4.txt index 70d1216fef..bfa357ca5a 100644 --- test/nfe/premd/save/pmd.4.txt +++ test/nfe/premd/save/pmd.4.txt @@ -1,66 +1,56 @@ # = NFE%PMD ================================================================== -# << anchor(1) : position = 3.000000,8.000000, 8.000000, 13.000000 +# << anchor(1) : position = 3.000000, 8.000000, 8.000000, 13.000000 # strength = 4.000000, 4.000000 >> # ----------------------------------------------------------------------------- # MD time (ps), CV(1:1) # ============================================================================= - 0.0000 8.01434902 - 0.0020 8.01663407 - 0.0040 8.01921042 - 0.0060 8.02219992 - 0.0080 8.02557460 - 0.0100 8.02917631 - 0.0100 8.02917631 - 0.0120 8.03279313 - 0.0140 8.03626193 - 0.0160 8.03955535 - 0.0180 8.04281144 - 0.0200 8.04626948 - 0.0200 8.04626948 - 0.0220 8.05013278 - 0.0240 8.05444189 - 0.0260 8.05904501 - 0.0280 8.06367755 - 0.0300 8.06808237 - 0.0300 8.06808237 - 0.0320 8.07209648 - 0.0340 8.07567699 - 0.0360 8.07887608 - 0.0380 8.08177951 - 0.0400 8.08443716 - 0.0400 8.08443716 - 0.0420 8.08682791 - 0.0440 8.08887636 - 0.0460 8.09050760 - 0.0480 8.09171840 - 0.0500 8.09263623 - 0.0500 8.09263623 - 0.0520 8.09352093 - 0.0540 8.09467902 - 0.0560 8.09633596 - 0.0580 8.09854119 - 0.0600 8.10113359 - 0.0600 8.10113359 - 0.0620 8.10376956 - 0.0640 8.10603430 - 0.0660 8.10762567 - 0.0680 8.10851609 - 0.0700 8.10897951 - 0.0700 8.10897951 - 0.0720 8.10946242 - 0.0740 8.11039084 - 0.0760 8.11202258 - 0.0780 8.11437902 - 0.0800 8.11723493 - 0.0800 8.11723493 - 0.0820 8.12016734 - 0.0840 8.12268174 - 0.0860 8.12438801 - 0.0880 8.12514740 - 0.0900 8.12511047 - 0.0900 8.12511047 - 0.0920 8.12462258 - 0.0940 8.12406970 - 0.0960 8.12376760 - 0.0980 8.12391802 - 0.1000 8.12459179 + 0.0000 6.51868743 + 0.0020 6.51885268 + 0.0040 6.51952249 + 0.0060 6.52049396 + 0.0080 6.52152833 + 0.0100 8.02900483 + 0.0120 8.03263060 + 0.0140 8.03611118 + 0.0160 8.03941501 + 0.0180 8.04267910 + 0.0200 8.04614535 + 0.0220 8.05002134 + 0.0240 8.05435132 + 0.0260 8.05898489 + 0.0280 8.06365612 + 0.0300 8.06810424 + 0.0320 8.07216166 + 0.0340 8.07578172 + 0.0360 8.07901520 + 0.0380 8.08194931 + 0.0400 8.08463719 + 0.0420 8.08706097 + 0.0440 8.08914666 + 0.0460 8.09081815 + 0.0480 8.09206861 + 0.0500 8.09302080 + 0.0520 8.09393096 + 0.0540 8.09510470 + 0.0560 8.09676971 + 0.0580 8.09897973 + 0.0600 8.10157799 + 0.0620 8.10422310 + 0.0640 8.10649888 + 0.0660 8.10809854 + 0.0680 8.10898931 + 0.0700 8.10944289 + 0.0720 8.10990758 + 0.0740 8.11081428 + 0.0760 8.11242702 + 0.0780 8.11477318 + 0.0800 8.11763166 + 0.0820 8.12058019 + 0.0840 8.12312068 + 0.0860 8.12485593 + 0.0880 8.12563937 + 0.0900 8.12561622 + 0.0920 8.12513056 + 0.0940 8.12457064 + 0.0960 8.12425655 + 0.0980 8.12439510 diff --git test/nfe/premd/save/pmd.4.txt.pmemd test/nfe/premd/save/pmd.4.txt.pmemd new file mode 100644 index 0000000000..2019d5ea56 --- /dev/null +++ test/nfe/premd/save/pmd.4.txt.pmemd @@ -0,0 +1,56 @@ +# = NFE%PMD ================================================================== +# << anchor(1) : position = 3.000000, 8.000000, 8.000000, 13.000000 +# strength = 4.000000, 4.000000 >> +# ----------------------------------------------------------------------------- +# MD time (ps), CV(1:1) +# ============================================================================= + 0.0000 6.30432743 + 0.0020 6.51885268 + 0.0040 6.51952249 + 0.0060 6.52049396 + 0.0080 6.52152833 + 0.0100 6.52243073 + 0.0120 8.03263060 + 0.0140 8.03611118 + 0.0160 8.03941501 + 0.0180 8.04267910 + 0.0200 8.04614535 + 0.0220 8.05002134 + 0.0240 8.05435132 + 0.0260 8.05898489 + 0.0280 8.06365612 + 0.0300 8.06810424 + 0.0320 8.07216166 + 0.0340 8.07578172 + 0.0360 8.07901520 + 0.0380 8.08194931 + 0.0400 8.08463719 + 0.0420 8.08706097 + 0.0440 8.08914666 + 0.0460 8.09081815 + 0.0480 8.09206861 + 0.0500 8.09302080 + 0.0520 8.09393096 + 0.0540 8.09510470 + 0.0560 8.09676971 + 0.0580 8.09897973 + 0.0600 8.10157799 + 0.0620 8.10422310 + 0.0640 8.10649888 + 0.0660 8.10809854 + 0.0680 8.10898931 + 0.0700 8.10944289 + 0.0720 8.10990758 + 0.0740 8.11081428 + 0.0760 8.11242702 + 0.0780 8.11477318 + 0.0800 8.11763166 + 0.0820 8.12058019 + 0.0840 8.12312068 + 0.0860 8.12485593 + 0.0880 8.12563937 + 0.0900 8.12561622 + 0.0920 8.12513056 + 0.0940 8.12457064 + 0.0960 8.12425655 + 0.0980 8.12439510 diff --git test/nfe/premd/save/rem.log test/nfe/premd/save/rem.log index 41a31fd7d6..09afc0cd48 100644 --- test/nfe/premd/save/rem.log +++ test/nfe/premd/save/rem.log @@ -3,54 +3,54 @@ # REMD filenames: # remlog= rem.log # remtype= rem.type -# Rep#, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate (i,i+1), ResStruct# +# Rep#, Neibr#, Temp0, PotE(x_1), PotE(x_2), left_fe, right_fe, Success, Success rate (i,i+1) # exchange 1 - 1 -1.00 0.00 -10152.55 320.00 320.00 0.00 -1 - 2 -1.00 0.00 -10313.68 300.00 300.00 0.00 -1 - 3 -1.00 0.00 -10131.41 330.00 330.00 0.00 -1 - 4 -1.00 0.00 -10184.84 310.00 310.00 0.00 -1 + 1 4 300.00 -10151.40 -10183.99 -3.24 0.00 T 0.00 + 2 3 310.00 -10311.81 -10127.35 0.00 1.66 F 0.00 + 3 2 320.00 -10129.86 -10313.48 -2.51 0.00 F 0.00 + 4 1 330.00 -10179.09 -10148.16 0.00 4.90 T 2.00 # exchange 2 - 1 -1.00 308.46 -10128.95 320.00 320.00 0.00 -1 - 2 -1.00 295.33 -10317.63 300.00 300.00 0.00 -1 - 3 -1.00 309.55 -10093.02 330.00 330.00 0.00 -1 - 4 -1.00 301.86 -10230.52 310.00 310.00 0.00 -1 + 1 2 300.00 -10290.92 -10314.76 -3.24 0.76 T 1.00 + 2 1 310.00 -10315.70 -10291.68 -0.94 1.66 T 0.00 + 3 4 320.00 -10091.52 -10057.23 -2.51 1.59 T 1.00 + 4 3 330.00 -10053.21 -10093.10 4.02 4.90 T 1.00 # exchange 3 - 1 -1.00 308.74 -10155.85 320.00 320.00 0.00 -1 - 2 -1.00 289.65 -10277.29 300.00 300.00 0.00 -1 - 3 -1.00 303.44 -10069.64 330.00 330.00 0.00 -1 - 4 -1.00 294.86 -10165.38 310.00 310.00 0.00 -1 + 1 4 300.00 -10297.31 -10041.81 1.50 0.76 F 0.67 + 2 3 310.00 -10220.02 -10089.45 -0.94 1.25 F 0.00 + 3 2 320.00 -10089.39 -10219.38 -0.37 1.59 F 0.67 + 4 1 330.00 -10046.44 -10299.23 4.02 4.45 F 0.67 # exchange 4 - 1 -1.00 313.60 -10164.50 320.00 320.00 0.00 -1 - 2 -1.00 285.00 -10250.62 300.00 300.00 0.00 -1 - 3 -1.00 307.50 -10076.25 330.00 330.00 0.00 -1 - 4 -1.00 291.94 -10166.22 310.00 310.00 0.00 -1 + 1 2 300.00 -10276.11 -10215.44 1.50 0.86 F 0.50 + 2 1 310.00 -10216.19 -10277.05 -0.84 1.25 F 0.00 + 3 4 320.00 -10103.67 -10046.80 -0.37 1.15 F 0.50 + 4 3 330.00 -10048.51 -10099.69 3.57 4.45 F 0.50 # exchange 5 - 1 -1.00 308.93 -10147.18 320.00 320.00 0.00 -1 - 2 -1.00 290.54 -10294.49 300.00 300.00 0.00 -1 - 3 -1.00 304.21 -10073.01 330.00 330.00 0.00 -1 - 4 -1.00 292.64 -10165.84 310.00 310.00 0.00 -1 + 1 4 300.00 -10318.76 -10039.91 1.63 0.86 F 0.40 + 2 3 310.00 -10217.35 -10088.28 -0.84 1.01 F 0.00 + 3 2 320.00 -10088.26 -10216.70 -0.21 1.15 F 0.40 + 4 1 330.00 -10044.65 -10320.58 3.57 4.18 F 0.40 # exchange 6 - 1 -1.00 306.64 -10125.62 320.00 320.00 0.00 -1 - 2 -1.00 288.34 -10257.34 300.00 300.00 0.00 -1 - 3 -1.00 310.27 -10105.01 330.00 330.00 0.00 -1 - 4 -1.00 299.16 -10192.37 310.00 310.00 0.00 -1 + 1 2 300.00 -10282.21 -10242.75 1.63 0.89 T 0.67 + 2 1 310.00 -10243.50 -10283.16 -0.81 1.01 T 0.00 + 3 4 320.00 -10062.29 -10076.51 -0.21 0.89 F 0.33 + 4 3 330.00 -10078.29 -10058.43 3.30 4.18 F 0.33 # exchange 7 - 1 -1.00 302.08 -10095.57 320.00 320.00 0.00 -1 - 2 -1.00 283.39 -10240.54 300.00 300.00 0.00 -1 - 3 -1.00 306.46 -10081.57 330.00 330.00 0.00 -1 - 4 -1.00 296.58 -10186.97 310.00 310.00 0.00 -1 + 1 4 300.00 -10262.32 -10047.35 1.46 0.89 F 0.57 + 2 3 310.00 -10246.27 -10024.87 -0.81 1.20 F 0.00 + 3 2 320.00 -10024.93 -10247.82 -0.17 0.89 F 0.29 + 4 1 330.00 -10052.13 -10257.26 3.30 3.99 F 0.29 # exchange 8 - 1 -1.00 299.23 -10078.43 320.00 320.00 0.00 -1 - 2 1.02 283.51 -10236.66 300.00 310.00 0.25 -1 - 3 -1.00 308.20 -10080.62 330.00 330.00 0.00 -1 - 4 0.98 301.32 -10202.87 310.00 300.00 0.00 -1 + 1 2 300.00 -10283.39 -10235.63 1.46 0.86 F 0.50 + 2 1 310.00 -10236.59 -10284.12 -0.84 1.20 F 0.00 + 3 4 320.00 -10012.16 -10049.48 -0.17 0.71 F 0.25 + 4 3 330.00 -10051.30 -10008.43 3.12 3.99 F 0.25 # exchange 9 - 1 -1.00 295.30 -10054.41 320.00 320.00 0.00 -1 - 2 -1.00 292.68 -10238.31 310.00 310.00 0.00 -1 - 3 -1.00 311.45 -10117.38 330.00 330.00 0.00 -1 - 4 -1.00 288.00 -10199.33 300.00 300.00 0.22 -1 + 1 4 300.00 -10263.99 -10081.76 1.32 0.86 F 0.44 + 2 3 310.00 -10262.32 -9985.35 -0.84 1.27 F 0.00 + 3 2 320.00 -9985.47 -10263.82 -0.16 0.71 F 0.22 + 4 1 330.00 -10086.59 -10258.77 3.12 3.84 F 0.22 # exchange 10 - 1 -1.00 298.26 -10079.60 320.00 320.00 0.00 -1 - 2 -1.00 290.34 -10217.17 310.00 310.00 0.00 -1 - 3 -1.00 309.27 -10081.68 330.00 330.00 0.00 -1 - 4 -1.00 293.44 -10222.59 300.00 300.00 0.20 -1 + 1 2 300.00 -10281.42 -10245.22 1.32 0.83 T 0.60 + 2 1 310.00 -10246.19 -10282.15 -0.87 1.27 T 0.00 + 3 4 320.00 -10010.13 -10048.70 -0.16 0.56 F 0.20 + 4 3 330.00 -10050.57 -10006.46 2.97 3.84 F 0.20 diff --git test/nfe/run-pmemd-parallel.sh test/nfe/run-pmemd-parallel.sh index 8815f6e71e..a7f469bf90 100755 --- test/nfe/run-pmemd-parallel.sh +++ test/nfe/run-pmemd-parallel.sh @@ -15,7 +15,7 @@ fi TESTS_2="abmd_ANALYSIS abmd_FLOODING abmd_UMBRELLA smd smd2 pmd" # 4*n mpi threads -TESTS_4="bbmd mwabmd" +TESTS_4="bbmd mwabmd premd abremd" TESTS="${TESTS_2} ${TESTS_4}" diff --git test/nfe/smd/run-pmemd.sh test/nfe/smd/run-pmemd.sh index bca1d6a8f4..516ecf66c3 100755 --- test/nfe/smd/run-pmemd.sh +++ test/nfe/smd/run-pmemd.sh @@ -28,7 +28,7 @@ cp -p ../inpcrd.4 ./inpcrd # run SANDER # -${SANDER_CMD} > sander.out 2>&1 +${SANDER_CMD} -O > sander.out 2>&1 ../../dacdif -t 1 save.pmemd/mdout mdout ../../dacdif -t 1 save.pmemd/smd.txt smd.txt diff --git test/nfe/smd/save.pmemd/mdout test/nfe/smd/save.pmemd/mdout index 2f50be32c2..96d2e9c879 100644 --- test/nfe/smd/save.pmemd/mdout +++ test/nfe/smd/save.pmemd/mdout @@ -1,15 +1,17 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 06/03/2016 at 19:55:33 +| Run on 09/05/2018 at 12:48:29 -| Executable path: /home/feng/git_feng/amber/bin/pmemd -| Working directory: /home/feng/git_feng/amber/test/nfe/smd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/smd +| Hostname: gaia.physics.ncsu.edu + + [-O]verwriting output File Assignments: | MDIN: mdin @@ -22,6 +24,7 @@ File Assignments: | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo +|LOGFILE: logfile | MDFRC: mdfrc @@ -34,7 +37,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &smd @@ -44,9 +47,11 @@ File Assignments: / +| irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: +| MPI | PUBFFT | BINTRAJ | EMIL @@ -136,6 +141,13 @@ Ewald parameters: Ewald Coefficient = 0.34864 Interpolation order = 4 +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- @@ -150,11 +162,14 @@ NGLY Forcing neutrality... | Dynamic Memory, Types Used: -| Reals 202260 -| Integers 79073 +| Reals 590421 +| Integers 203216 + +| Nonbonded Pairs Initial Allocation: 89574 -| Nonbonded Pairs Initial Allocation: 524959 +| Running AMBER/MPI version on 16 MPI task + -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- @@ -231,103 +246,144 @@ NGLY NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.4841 EKtot = 1914.1816 EPtot = -10235.6657 + Etot = -8321.4806 EKtot = 1914.1816 EPtot = -10235.6622 BOND = 19.0733 ANGLE = 63.5926 DIHED = 72.6962 1-4 NB = 31.9325 1-4 EEL = 541.0003 VDWAALS = 1297.2732 - EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0035 + EAMBER (non-restraint) = -10235.6657 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.004 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.14 PRESS = 0.0 - Etot = -8329.3462 EKtot = 1917.1534 EPtot = -10246.4996 + Etot = -8329.2146 EKtot = 1917.1534 EPtot = -10246.3679 BOND = 25.2705 ANGLE = 68.1031 DIHED = 73.1051 1-4 NB = 34.0181 1-4 EEL = 541.6468 VDWAALS = 1326.2606 - EELEC = -12314.9039 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9039 EHBOND = 0.0000 RESTRAINT = 0.1317 + EAMBER (non-restraint) = -10246.4996 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.132 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 - Etot = -8320.0935 EKtot = 1879.6469 EPtot = -10199.7404 + Etot = -8319.2928 EKtot = 1879.6469 EPtot = -10198.9398 BOND = 25.7140 ANGLE = 67.6930 DIHED = 76.2940 1-4 NB = 31.4982 1-4 EEL = 535.0701 VDWAALS = 1359.5148 - EELEC = -12295.5246 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12295.5246 EHBOND = 0.0000 RESTRAINT = 0.8007 + EAMBER (non-restraint) = -10199.7404 Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.801 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.16 PRESS = 0.0 - Etot = -8311.9741 EKtot = 1891.9866 EPtot = -10203.9607 + Etot = -8309.1693 EKtot = 1891.9866 EPtot = -10201.1559 BOND = 32.8142 ANGLE = 68.2241 DIHED = 72.9022 1-4 NB = 28.4181 1-4 EEL = 536.5080 VDWAALS = 1387.0572 - EELEC = -12329.8844 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12329.8844 EHBOND = 0.0000 RESTRAINT = 2.8048 + EAMBER (non-restraint) = -10203.9607 Ewald error estimate: 0.2629E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 2.805 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.78 PRESS = 0.0 - Etot = -8313.6979 EKtot = 1908.5486 EPtot = -10222.2465 + Etot = -8306.4442 EKtot = 1908.5486 EPtot = -10214.9928 BOND = 35.4065 ANGLE = 70.7948 DIHED = 73.4499 1-4 NB = 28.9563 1-4 EEL = 539.1442 VDWAALS = 1406.7852 - EELEC = -12376.7834 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12376.7834 EHBOND = 0.0000 RESTRAINT = 7.2537 + EAMBER (non-restraint) = -10222.2465 Ewald error estimate: 0.3091E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 7.254 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.87 PRESS = 0.0 - Etot = -8308.4107 EKtot = 1947.0569 EPtot = -10255.4675 + Etot = -8293.1617 EKtot = 1947.0569 EPtot = -10240.2185 BOND = 32.4478 ANGLE = 64.3517 DIHED = 74.4051 1-4 NB = 30.3467 1-4 EEL = 535.0802 VDWAALS = 1408.0681 - EELEC = -12400.1671 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12400.1671 EHBOND = 0.0000 RESTRAINT = 15.2490 + EAMBER (non-restraint) = -10255.4675 Ewald error estimate: 0.7051E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 15.249 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 296.03 PRESS = 0.0 - Etot = -8312.1750 EKtot = 1872.1481 EPtot = -10184.3231 + Etot = -8288.3884 EKtot = 1872.1481 EPtot = -10160.5366 BOND = 23.6203 ANGLE = 70.4617 DIHED = 73.4533 1-4 NB = 30.4186 1-4 EEL = 532.1672 VDWAALS = 1412.0691 - EELEC = -12326.5133 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12326.5133 EHBOND = 0.0000 RESTRAINT = 23.7866 + EAMBER (non-restraint) = -10184.3231 Ewald error estimate: 0.8162E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 23.787 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.16 PRESS = 0.0 - Etot = -8315.7220 EKtot = 1898.2612 EPtot = -10213.9832 + Etot = -8285.1676 EKtot = 1898.2612 EPtot = -10183.4288 BOND = 27.2716 ANGLE = 63.0108 DIHED = 74.5673 1-4 NB = 35.0604 1-4 EEL = 532.7362 VDWAALS = 1410.9158 - EELEC = -12357.5454 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12357.5454 EHBOND = 0.0000 RESTRAINT = 30.5544 + EAMBER (non-restraint) = -10213.9832 Ewald error estimate: 0.3162E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 30.554 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 299.04 PRESS = 0.0 - Etot = -8319.8351 EKtot = 1891.2068 EPtot = -10211.0419 + Etot = -8283.7557 EKtot = 1891.2068 EPtot = -10174.9625 BOND = 28.1955 ANGLE = 58.9520 DIHED = 74.4894 1-4 NB = 36.3310 1-4 EEL = 535.6839 VDWAALS = 1407.6836 - EELEC = -12352.3773 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12352.3773 EHBOND = 0.0000 RESTRAINT = 36.0794 + EAMBER (non-restraint) = -10211.0419 Ewald error estimate: 0.1464E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 36.079 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.29 PRESS = 0.0 - Etot = -8321.7739 EKtot = 1930.7095 EPtot = -10252.4834 + Etot = -8283.7983 EKtot = 1930.7095 EPtot = -10214.5078 BOND = 22.4456 ANGLE = 69.8727 DIHED = 71.3491 1-4 NB = 36.2373 1-4 EEL = 538.1544 VDWAALS = 1393.6104 - EELEC = -12384.1528 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12384.1528 EHBOND = 0.0000 RESTRAINT = 37.9756 + EAMBER (non-restraint) = -10252.4834 Ewald error estimate: 0.3092E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 37.976 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 301.24 PRESS = 0.0 - Etot = -8317.4513 EKtot = 1905.0900 EPtot = -10222.5412 + Etot = -8301.9873 EKtot = 1905.0900 EPtot = -10207.0773 BOND = 27.2259 ANGLE = 66.5057 DIHED = 73.6712 1-4 NB = 32.3217 1-4 EEL = 536.7191 VDWAALS = 1380.9238 - EELEC = -12339.9086 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12339.9086 EHBOND = 0.0000 RESTRAINT = 15.4639 + EAMBER (non-restraint) = -10222.5412 Ewald error estimate: 0.1416E-03 ------------------------------------------------------------------------------ @@ -336,10 +392,11 @@ NGLY NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.46 PRESS = 0.0 - Etot = 5.8801 EKtot = 21.9119 EPtot = 22.9308 + Etot = 16.4353 EKtot = 21.9119 EPtot = 27.2672 BOND = 4.8455 ANGLE = 3.6701 DIHED = 1.2744 1-4 NB = 2.7695 1-4 EEL = 3.0603 VDWAALS = 38.2540 - EELEC = 40.5952 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 40.5952 EHBOND = 0.0000 RESTRAINT = 14.6478 + EAMBER (non-restraint) = 12.6194 Ewald error estimate: 0.1610E-03 ------------------------------------------------------------------------------ @@ -347,66 +404,77 @@ NGLY 5. TIMINGS -------------------------------------------------------------------------------- -| NonSetup CPU Time in Major Routines: +| NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ -| Nonbond 1.31 91.80 +| DataDistrib 0.05 36.82 +| Nonbond 0.06 39.27 | Bond 0.00 0.00 -| Angle 0.00 0.21 -| Dihedral 0.01 0.63 -| Shake 0.01 0.91 -| RunMD 0.09 6.31 -| Other 0.00 0.14 +| Angle 0.00 0.13 +| Dihedral 0.00 0.39 +| Shake 0.00 0.35 +| RunMD 0.03 22.34 +| Other 0.00 0.70 | ------------------------------ -| Total 1.43 +| Total 0.14 -| PME Nonbond Pairlist CPU Time: +| PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| Set Up Cit 0.00 0.28 -| Build List 0.23 16.33 +| Set Up Cit 0.00 0.48 +| Build List 0.00 3.23 | --------------------------------- -| Total 0.24 16.61 +| Total 0.01 3.71 -| PME Direct Force CPU Time: +| PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| NonBonded Calc 0.72 50.32 -| Exclude Masked 0.01 0.70 -| Other 0.01 0.77 +| NonBonded Calc 0.03 20.94 +| Exclude Masked 0.00 0.48 +| Other 0.00 0.83 | --------------------------------- -| Total 0.74 51.79 +| Total 0.03 22.25 -| PME Reciprocal Force CPU Time: +| PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- -| 1D bspline 0.03 2.31 -| Grid Charges 0.03 1.89 -| Scalar Sum 0.07 4.70 -| Gradient Sum 0.04 2.73 -| FFT 0.17 11.77 +| 1D bspline 0.00 1.09 +| Grid Charges 0.00 1.18 +| Scalar Sum 0.00 1.53 +| Gradient Sum 0.00 1.48 +| FFT 0.01 7.64 | --------------------------------- -| Total 0.33 23.41 +| Total 0.02 12.91 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.17 +| FFT Reassign 0.00 0.22 +| ------------------------------------ +| Total 0.00 0.39 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 45 steps: -| Elapsed(s) = 1.28 Per Step(ms) = 28.37 -| ns/day = 6.09 seconds/ns = 14187.37 +| Elapsed(s) = 0.11 Per Step(ms) = 2.46 +| ns/day = 70.29 seconds/ns = 1229.12 | | Average timings for all steps: -| Elapsed(s) = 1.47 Per Step(ms) = 29.32 -| ns/day = 5.89 seconds/ns = 14658.40 +| Elapsed(s) = 0.15 Per Step(ms) = 2.95 +| ns/day = 58.64 seconds/ns = 1473.47 | ----------------------------------------------------- -| Setup CPU time: 0.07 seconds -| NonSetup CPU time: 1.43 seconds -| Total CPU time: 1.50 seconds 0.00 hours +| Master Setup CPU time: 0.05 seconds +| Master NonSetup CPU time: 0.15 seconds +| Master Total CPU time: 0.20 seconds 0.00 hours -| Setup wall time: 0 seconds -| NonSetup wall time: 1 seconds -| Total wall time: 1 seconds 0.00 hours +| Master Setup wall time: 1 seconds +| Master NonSetup wall time: 0 seconds +| Master Total wall time: 1 seconds 0.00 hours diff --git test/nfe/smd/save.sander/mdout test/nfe/smd/save.sander/mdout index 629319303e..4fb1be7649 100644 --- test/nfe/smd/save.sander/mdout +++ test/nfe/smd/save.sander/mdout @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/10/2016 at 16:57:39 +| Run on 09/03/2018 at 11:40:21 -| Executable path: /home/feng/git_feng/amber/bin/sander -| Working directory: /home/feng/git_feng/amber/test/nfe/smd -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/smd +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -28,6 +28,14 @@ File Assignments: |RSTDIP: rstdip |INPTRA: inptraj +| REMLOG: rem.log +| REMTYPE: rem.type +| REMSTRIP: +| SAVEENE: saveene +|CLUSTERINF: cluster.info +| RESERVOIR: reserv/frame +| REMDDIM: + Here is the input file: @@ -38,7 +46,7 @@ File Assignments: ntt = 3, gamma_ln = 1.0, ntf = 2, ntc = 2, tol = 0.00001, cut = 8.0, dt = 0.002, ig = 71277, - ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, + ntpr = 5, ntwx = 0, nstlim = 50, infe = 1, / &smd @@ -51,7 +59,7 @@ File Assignments: 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: +| Flags: MPI getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -69,13 +77,13 @@ File Assignments: | Memory Use Allocated -| Real 294892 +| Real 304361 | Hollerith 10444 | Integer 115557 -| Max Pairs 1047666 +| Max Pairs 261916 | nblistReal 37716 -| nblist Int 118089 -| Total 7644 kbytes +| nblist Int 105664 +| Total 4600 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. @@ -134,6 +142,9 @@ Ewald parameters: Ewald Coefficient = 0.34864 Interpolation order = 4 +| MPI Timing options: +| profile_mpi = 0 + -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- @@ -142,9 +153,14 @@ NGLY begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 1001 +| Atom division among processors: +| 0 392 785 1178 1568 1961 2354 2744 +| 3143 Sum of charges from parm topology file = -0.00000001 Forcing neutrality... +| Running AMBER/MPI version on 8 nodes + -------------------------------------------------------------------------------- 4. RESULTS @@ -216,107 +232,148 @@ NGLY | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- -| Local SIZE OF NONBOND LIST = 650668 +| Local SIZE OF NONBOND LIST = 84063 | TOTAL SIZE OF NONBOND LIST = 650668 NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 302.67 PRESS = 0.0 - Etot = -8321.4841 EKtot = 1914.1816 EPtot = -10235.6657 + Etot = -8321.4806 EKtot = 1914.1816 EPtot = -10235.6622 BOND = 19.0733 ANGLE = 63.5926 DIHED = 72.6962 1-4 NB = 31.9325 1-4 EEL = 541.0003 VDWAALS = 1297.2732 - EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12261.2338 EHBOND = 0.0000 RESTRAINT = 0.0035 + EAMBER (non-restraint) = -10235.6657 Ewald error estimate: 0.5638E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.004 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 303.14 PRESS = 0.0 - Etot = -8329.3462 EKtot = 1917.1534 EPtot = -10246.4996 + Etot = -8329.2146 EKtot = 1917.1534 EPtot = -10246.3679 BOND = 25.2705 ANGLE = 68.1031 DIHED = 73.1051 1-4 NB = 34.0181 1-4 EEL = 541.6468 VDWAALS = 1326.2606 - EELEC = -12314.9039 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12314.9039 EHBOND = 0.0000 RESTRAINT = 0.1317 + EAMBER (non-restraint) = -10246.4996 Ewald error estimate: 0.2917E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.132 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 297.21 PRESS = 0.0 - Etot = -8320.0935 EKtot = 1879.6469 EPtot = -10199.7404 + Etot = -8319.2928 EKtot = 1879.6469 EPtot = -10198.9398 BOND = 25.7140 ANGLE = 67.6930 DIHED = 76.2940 1-4 NB = 31.4982 1-4 EEL = 535.0701 VDWAALS = 1359.5148 - EELEC = -12295.5246 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12295.5246 EHBOND = 0.0000 RESTRAINT = 0.8007 + EAMBER (non-restraint) = -10199.7404 Ewald error estimate: 0.1426E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.801 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 299.16 PRESS = 0.0 - Etot = -8311.9741 EKtot = 1891.9866 EPtot = -10203.9607 + Etot = -8309.1693 EKtot = 1891.9866 EPtot = -10201.1559 BOND = 32.8142 ANGLE = 68.2241 DIHED = 72.9022 1-4 NB = 28.4181 1-4 EEL = 536.5080 VDWAALS = 1387.0572 - EELEC = -12329.8844 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12329.8844 EHBOND = 0.0000 RESTRAINT = 2.8048 + EAMBER (non-restraint) = -10203.9607 Ewald error estimate: 0.2629E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 2.805 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 301.78 PRESS = 0.0 - Etot = -8313.6979 EKtot = 1908.5486 EPtot = -10222.2465 + Etot = -8306.4442 EKtot = 1908.5486 EPtot = -10214.9928 BOND = 35.4065 ANGLE = 70.7948 DIHED = 73.4499 1-4 NB = 28.9563 1-4 EEL = 539.1442 VDWAALS = 1406.7852 - EELEC = -12376.7834 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12376.7834 EHBOND = 0.0000 RESTRAINT = 7.2537 + EAMBER (non-restraint) = -10222.2465 Ewald error estimate: 0.3091E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 7.254 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = 307.87 PRESS = 0.0 - Etot = -8308.4107 EKtot = 1947.0569 EPtot = -10255.4675 + Etot = -8293.1617 EKtot = 1947.0569 EPtot = -10240.2185 BOND = 32.4478 ANGLE = 64.3517 DIHED = 74.4051 1-4 NB = 30.3467 1-4 EEL = 535.0802 VDWAALS = 1408.0681 - EELEC = -12400.1671 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12400.1671 EHBOND = 0.0000 RESTRAINT = 15.2490 + EAMBER (non-restraint) = -10255.4675 Ewald error estimate: 0.7051E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 15.249 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 35 TIME(PS) = 0.070 TEMP(K) = 296.03 PRESS = 0.0 - Etot = -8312.1750 EKtot = 1872.1481 EPtot = -10184.3231 + Etot = -8288.3884 EKtot = 1872.1481 EPtot = -10160.5366 BOND = 23.6203 ANGLE = 70.4617 DIHED = 73.4533 1-4 NB = 30.4186 1-4 EEL = 532.1672 VDWAALS = 1412.0691 - EELEC = -12326.5133 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12326.5133 EHBOND = 0.0000 RESTRAINT = 23.7866 + EAMBER (non-restraint) = -10184.3231 Ewald error estimate: 0.8162E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 23.787 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = 300.16 PRESS = 0.0 - Etot = -8315.7220 EKtot = 1898.2612 EPtot = -10213.9832 + Etot = -8285.1676 EKtot = 1898.2612 EPtot = -10183.4288 BOND = 27.2716 ANGLE = 63.0108 DIHED = 74.5673 1-4 NB = 35.0604 1-4 EEL = 532.7362 VDWAALS = 1410.9158 - EELEC = -12357.5454 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12357.5454 EHBOND = 0.0000 RESTRAINT = 30.5544 + EAMBER (non-restraint) = -10213.9832 Ewald error estimate: 0.3162E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 30.554 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 45 TIME(PS) = 0.090 TEMP(K) = 299.04 PRESS = 0.0 - Etot = -8319.8351 EKtot = 1891.2068 EPtot = -10211.0419 + Etot = -8283.7557 EKtot = 1891.2068 EPtot = -10174.9625 BOND = 28.1955 ANGLE = 58.9520 DIHED = 74.4894 1-4 NB = 36.3310 1-4 EEL = 535.6839 VDWAALS = 1407.6836 - EELEC = -12352.3773 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12352.3773 EHBOND = 0.0000 RESTRAINT = 36.0794 + EAMBER (non-restraint) = -10211.0419 Ewald error estimate: 0.1464E-03 ------------------------------------------------------------------------------ + NFE restraints: SMD : 36.079 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 305.29 PRESS = 0.0 - Etot = -8321.7739 EKtot = 1930.7095 EPtot = -10252.4834 + Etot = -8283.7983 EKtot = 1930.7095 EPtot = -10214.5078 BOND = 22.4456 ANGLE = 69.8727 DIHED = 71.3491 1-4 NB = 36.2373 1-4 EEL = 538.1544 VDWAALS = 1393.6104 - EELEC = -12384.1528 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12384.1528 EHBOND = 0.0000 RESTRAINT = 37.9756 + EAMBER (non-restraint) = -10252.4834 Ewald error estimate: 0.3092E-04 ------------------------------------------------------------------------------ + NFE restraints: SMD : 37.976 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 50 S T E P S NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 300.66 PRESS = 0.0 - Etot = -8317.1552 EKtot = 1901.4201 EPtot = -10218.5753 + Etot = -8303.2118 EKtot = 1901.4201 EPtot = -10204.6319 BOND = 28.7364 ANGLE = 67.4458 DIHED = 73.7698 1-4 NB = 32.2129 1-4 EEL = 536.8348 VDWAALS = 1376.1742 - EELEC = -12333.7492 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = -12333.7492 EHBOND = 0.0000 RESTRAINT = 13.9434 + EAMBER (non-restraint) = -10218.5753 Ewald error estimate: 0.1704E-03 ------------------------------------------------------------------------------ @@ -325,10 +382,11 @@ NGLY NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 3.24 PRESS = 0.0 - Etot = 6.8192 EKtot = 20.4780 EPtot = 20.5683 + Etot = 17.2530 EKtot = 20.4780 EPtot = 26.4430 BOND = 4.5953 ANGLE = 4.1271 DIHED = 1.9574 1-4 NB = 2.6129 1-4 EEL = 3.2599 VDWAALS = 43.5258 - EELEC = 42.4339 EHBOND = 0.0000 RESTRAINT = 0.0000 + EELEC = 42.4339 EHBOND = 0.0000 RESTRAINT = 14.1970 + EAMBER (non-restraint) = 12.2460 Ewald error estimate: 0.1604E-03 ------------------------------------------------------------------------------ @@ -337,51 +395,58 @@ NGLY 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.37% of Total) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.00 ( 0.24% of Total) | Fast Water setup 0.00 ( 0.01% of Total) -| Build the list 0.30 (91.18% of List ) -| Other 0.03 ( 8.82% of List ) -| List time 0.33 (11.91% of Nonbo) -| Short_ene time 1.85 (99.14% of Direc) -| Other 0.02 ( 0.86% of Direc) -| Direct Ewald time 1.87 (77.22% of Ewald) -| Adjust Ewald time 0.01 ( 0.62% of Ewald) +| Build the list 0.02 (62.30% of List ) +| Other 0.01 (37.70% of List ) +| List time 0.04 (15.45% of Nonbo) +| Short_ene time 0.13 (95.15% of Direc) +| Other 0.01 ( 4.85% of Direc) +| Direct Ewald time 0.14 (69.38% of Ewald) +| Adjust Ewald time 0.00 ( 0.46% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.02 ( 3.58% of Recip) -| Fill charge grid 0.04 ( 7.32% of Recip) -| Scalar sum 0.22 (41.55% of Recip) -| Grad sum 0.09 (16.34% of Recip) -| FFT time 0.17 (31.19% of Recip) -| Other 0.00 ( 0.02% of Recip) -| Recip Ewald time 0.53 (22.03% of Ewald) -| Force Adjust 0.00 ( 0.02% of Ewald) -| Virial junk 0.00 ( 0.04% of Ewald) -| Other 0.00 ( 0.07% of Ewald) -| Ewald time 2.42 (88.08% of Nonbo) -| Nonbond force 2.75 (99.39% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.45% of Force) -| Other 0.00 ( 0.16% of Force) -| Force time 2.77 (96.27% of Runmd) -| Shake time 0.02 ( 0.58% of Runmd) -| Verlet update time 0.09 ( 3.06% of Runmd) -| Other 0.00 ( 0.10% of Runmd) -| Runmd Time 2.87 (98.05% of Total) -| Other 0.05 ( 1.57% of Total) -| Total time 2.93 (99.90% of ALL ) +| Fill Bspline coeffs 0.00 ( 9.57% of Recip) +| Fill charge grid 0.00 ( 6.55% of Recip) +| Scalar sum 0.01 (27.86% of Recip) +| Grad sum 0.01 (13.75% of Recip) +| FFT back comm time 0.00 (12.84% of FFT t) +| Other 0.02 (87.16% of FFT t) +| FFT time 0.02 (38.99% of Recip) +| Other 0.00 ( 3.28% of Recip) +| Recip Ewald time 0.05 (25.32% of Ewald) +| Force Adjust 0.01 ( 4.21% of Ewald) +| Virial junk 0.00 ( 0.51% of Ewald) +| Start synchronizatio 0.00 ( 0.01% of Ewald) +| Other 0.00 ( 0.10% of Ewald) +| Ewald time 0.20 (84.54% of Nonbo) +| Other 0.00 ( 0.01% of Nonbo) +| Nonbond force 0.23 (96.71% of Force) +| Bond/Angle/Dihedral 0.00 ( 0.43% of Force) +| FRC Collect time 0.00 ( 0.81% of Force) +| Other 0.00 ( 2.05% of Force) +| Force time 0.24 (82.40% of Runmd) +| Shake time 0.00 ( 0.42% of Runmd) +| Verlet update time 0.05 (15.94% of Runmd) +| CRD distribute time 0.00 ( 0.35% of Runmd) +| Other 0.00 ( 0.89% of Runmd) +| Runmd Time 0.29 (87.88% of Total) +| Other 0.04 (11.88% of Total) +| Total time 0.33 (99.68% of ALL ) | Number of list builds : 5 -| Highest rstack allocated: 193099 -| Highest istack allocated: 3143 +| Highest rstack allocated: 41935 +| Highest istack allocated: 931 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 2.87 Per Step(ms) = 57.46 -| ns/day = 3.01 seconds/ns = 28727.71 +| Elapsed(s) = 0.30 Per Step(ms) = 5.90 +| ns/day = 29.27 seconds/ns = 2951.43 | ----------------------------------------------------- -| Job began at 16:57:39.563 on 06/10/2016 -| Setup done at 16:57:39.623 on 06/10/2016 -| Run done at 16:57:42.496 on 06/10/2016 -| wallclock() was called 2233 times +| Job began at 11:40:21.821 on 09/03/2018 +| Setup done at 11:40:21.863 on 09/03/2018 +| Run done at 11:40:22.158 on 09/03/2018 +| wallclock() was called 2783 times diff --git test/nfe/smd2/run-sander.sh test/nfe/smd2/run-sander.sh index 35d7c5bac8..f3f32ddd48 100755 --- test/nfe/smd2/run-sander.sh +++ test/nfe/smd2/run-sander.sh @@ -16,7 +16,7 @@ if [ "$numprocs" -gt 6 ] ; then fi -set_SANDER sander +set_SANDER sander.MPI set_SANDER_CMD 1 JUNK="mdout mdinfo restrt work.txt sander.out" diff --git test/nfe/smd2/save.pmemd/mdout test/nfe/smd2/save.pmemd/mdout index bbcb9d2c28..944eded4d0 100644 --- test/nfe/smd2/save.pmemd/mdout +++ test/nfe/smd2/save.pmemd/mdout @@ -1,15 +1,15 @@ ------------------------------------------------------- - Amber 16 PMEMD 2016 + Amber 18 PMEMD 2018 ------------------------------------------------------- -| PMEMD implementation of SANDER, Release 16 +| PMEMD implementation of SANDER, Release 18 -| Run on 06/07/2016 at 18:06:56 +| Run on 09/05/2018 at 12:50:49 -| Executable path: /home/feng/git_feng/amber/bin/pmemd.MPI -| Working directory: /home/feng/git_feng/amber/test/nfe/smd2 -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/pmemd.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/smd2 +| Hostname: gaia.physics.ncsu.edu File Assignments: | MDIN: mdin @@ -34,7 +34,7 @@ File Assignments: irest = 1, ntx = 5, ntc = 2, ntf = 2, tol = 0.000001, ioutfm = 1, igb = 2, gbsa = 1, dt = 0.002, ntpr = 50, ntwx = 0, ntwr = 500, nstlim = 500, - ig = 29166, ntr = 0, nscm = 5000, infe = 1, + ig = 29166, ntr = 0, nscm = 5000, infe = 1, / &smd @@ -44,6 +44,7 @@ File Assignments: / +| irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: | MPI @@ -137,7 +138,7 @@ ACE Number of triangulated 3-point waters found: 0 | Dynamic Memory, Types Used: | Reals 4118 -| Integers 111594 +| Integers 112085 | Running AMBER/MPI version on 4 MPI task @@ -169,103 +170,144 @@ ACE NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 275.94 PRESS = 0.0 - Etot = 167.4983 EKtot = 55.9319 EPtot = 111.5664 + Etot = 169.1572 EKtot = 55.9319 EPtot = 113.2252 BOND = 15.8568 ANGLE = 52.2629 DIHED = 86.8661 1-4 NB = 16.2049 1-4 EEL = 287.9575 VDWAALS = -10.9421 - EELEC = -291.1708 EGB = -49.0562 RESTRAINT = 0.0000 + EELEC = -291.1708 EGB = -49.0562 RESTRAINT = 1.6588 + EAMBER (non-restraint) = 111.5664 ESURF= 3.5873 ------------------------------------------------------------------------------ + NFE restraints: SMD : 1.659 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 288.45 PRESS = 0.0 - Etot = 170.7038 EKtot = 58.4669 EPtot = 112.2370 + Etot = 175.4897 EKtot = 58.4669 EPtot = 117.0229 BOND = 14.4795 ANGLE = 60.0408 DIHED = 85.7967 1-4 NB = 14.1420 1-4 EEL = 282.7831 VDWAALS = -11.3633 - EELEC = -290.0343 EGB = -47.1461 RESTRAINT = 0.0000 + EELEC = -290.0343 EGB = -47.1461 RESTRAINT = 4.7859 + EAMBER (non-restraint) = 112.2370 ESURF= 3.5386 ------------------------------------------------------------------------------ + NFE restraints: SMD : 4.786 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 150 TIME(PS) = 0.300 TEMP(K) = 289.60 PRESS = 0.0 - Etot = 177.4099 EKtot = 58.7009 EPtot = 118.7090 + Etot = 179.8021 EKtot = 58.7009 EPtot = 121.1011 BOND = 13.9542 ANGLE = 52.9962 DIHED = 105.0150 1-4 NB = 12.6748 1-4 EEL = 282.4215 VDWAALS = -15.5026 - EELEC = -290.6914 EGB = -45.6790 RESTRAINT = 0.0000 + EELEC = -290.6914 EGB = -45.6790 RESTRAINT = 2.3922 + EAMBER (non-restraint) = 118.7090 ESURF= 3.5203 ------------------------------------------------------------------------------ + NFE restraints: SMD : 2.392 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 200 TIME(PS) = 0.400 TEMP(K) = 302.89 PRESS = 0.0 - Etot = 180.9301 EKtot = 61.3929 EPtot = 119.5372 + Etot = 183.7139 EKtot = 61.3929 EPtot = 122.3210 BOND = 16.5717 ANGLE = 47.3139 DIHED = 107.4803 1-4 NB = 14.8982 1-4 EEL = 286.3698 VDWAALS = -16.9853 - EELEC = -293.6555 EGB = -45.9481 RESTRAINT = 0.0000 + EELEC = -293.6555 EGB = -45.9481 RESTRAINT = 2.7837 + EAMBER (non-restraint) = 119.5372 ESURF= 3.4923 ------------------------------------------------------------------------------ + NFE restraints: SMD : 2.784 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 250 TIME(PS) = 0.500 TEMP(K) = 260.88 PRESS = 0.0 - Etot = 187.1558 EKtot = 52.8786 EPtot = 134.2772 + Etot = 187.9272 EKtot = 52.8786 EPtot = 135.0486 BOND = 17.1069 ANGLE = 62.2403 DIHED = 104.7649 1-4 NB = 15.0971 1-4 EEL = 289.5548 VDWAALS = -16.7702 - EELEC = -297.1551 EGB = -44.0727 RESTRAINT = 0.0000 + EELEC = -297.1551 EGB = -44.0727 RESTRAINT = 0.7714 + EAMBER (non-restraint) = 134.2772 ESURF= 3.5113 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.771 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 300 TIME(PS) = 0.600 TEMP(K) = 282.22 PRESS = 0.0 - Etot = 184.4709 EKtot = 57.2035 EPtot = 127.2675 + Etot = 184.5451 EKtot = 57.2035 EPtot = 127.3416 BOND = 17.2748 ANGLE = 55.5762 DIHED = 107.2426 1-4 NB = 12.2918 1-4 EEL = 286.0311 VDWAALS = -15.5175 - EELEC = -294.7725 EGB = -44.3639 RESTRAINT = 0.0000 + EELEC = -294.7725 EGB = -44.3639 RESTRAINT = 0.0742 + EAMBER (non-restraint) = 127.2675 ESURF= 3.5049 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.074 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 350 TIME(PS) = 0.700 TEMP(K) = 330.80 PRESS = 0.0 - Etot = 182.3983 EKtot = 67.0512 EPtot = 115.3471 + Etot = 184.0704 EKtot = 67.0512 EPtot = 117.0192 BOND = 12.9716 ANGLE = 51.7927 DIHED = 101.1596 1-4 NB = 13.2004 1-4 EEL = 285.4573 VDWAALS = -15.7416 - EELEC = -293.3998 EGB = -43.6556 RESTRAINT = 0.0000 + EELEC = -293.3998 EGB = -43.6556 RESTRAINT = 1.6721 + EAMBER (non-restraint) = 115.3471 ESURF= 3.5624 ------------------------------------------------------------------------------ + NFE restraints: SMD : 1.672 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = 306.12 PRESS = 0.0 - Etot = 179.5992 EKtot = 62.0495 EPtot = 117.5497 + Etot = 179.7182 EKtot = 62.0495 EPtot = 117.6688 BOND = 17.3184 ANGLE = 50.0925 DIHED = 100.9027 1-4 NB = 14.3564 1-4 EEL = 283.5260 VDWAALS = -14.9441 - EELEC = -294.6974 EGB = -42.5575 RESTRAINT = 0.0000 + EELEC = -294.6974 EGB = -42.5575 RESTRAINT = 0.1191 + EAMBER (non-restraint) = 117.5497 ESURF= 3.5529 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.119 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 450 TIME(PS) = 0.900 TEMP(K) = 278.28 PRESS = 0.0 - Etot = 170.9088 EKtot = 56.4060 EPtot = 114.5028 + Etot = 172.4252 EKtot = 56.4060 EPtot = 116.0192 BOND = 19.9606 ANGLE = 61.7312 DIHED = 83.1469 1-4 NB = 12.8673 1-4 EEL = 281.1143 VDWAALS = -13.5707 - EELEC = -291.4499 EGB = -42.8847 RESTRAINT = 0.0000 + EELEC = -291.4499 EGB = -42.8847 RESTRAINT = 1.5164 + EAMBER (non-restraint) = 114.5028 ESURF= 3.5877 ------------------------------------------------------------------------------ + NFE restraints: SMD : 1.516 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 274.14 PRESS = 0.0 - Etot = 170.0523 EKtot = 55.5658 EPtot = 114.4865 + Etot = 170.0691 EKtot = 55.5658 EPtot = 114.5033 BOND = 9.9899 ANGLE = 60.6437 DIHED = 86.9794 1-4 NB = 17.4990 1-4 EEL = 282.7687 VDWAALS = -11.7593 - EELEC = -292.4142 EGB = -42.8089 RESTRAINT = 0.0000 + EELEC = -292.4142 EGB = -42.8089 RESTRAINT = 0.0168 + EAMBER (non-restraint) = 114.4865 ESURF= 3.5882 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.017 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 10 S T E P S NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 288.93 PRESS = 0.0 - Etot = 177.1127 EKtot = 58.5647 EPtot = 118.5480 + Etot = 178.6918 EKtot = 58.5647 EPtot = 120.1271 BOND = 15.5484 ANGLE = 55.4690 DIHED = 96.9354 1-4 NB = 14.3232 1-4 EEL = 284.7984 VDWAALS = -14.3097 - EELEC = -292.9441 EGB = -44.8173 RESTRAINT = 0.0000 + EELEC = -292.9441 EGB = -44.8173 RESTRAINT = 1.5791 + EAMBER (non-restraint) = 118.5480 ESURF= 3.5446 ------------------------------------------------------------------------------ @@ -274,10 +316,11 @@ ACE NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 18.91 PRESS = 0.0 - Etot = 6.5241 EKtot = 3.8335 EPtot = 6.7610 + Etot = 6.2512 EKtot = 3.8335 EPtot = 6.3399 BOND = 2.6528 ANGLE = 5.0801 DIHED = 9.4462 1-4 NB = 1.5753 1-4 EEL = 2.5700 VDWAALS = 2.1359 - EELEC = 2.0991 EGB = 2.0099 RESTRAINT = 0.0000 + EELEC = 2.0991 EGB = 2.0099 RESTRAINT = 1.4108 + EAMBER (non-restraint) = 4.9290 ESURF= 0.0347 ------------------------------------------------------------------------------ @@ -289,43 +332,43 @@ ACE | | Routine Sec % | ------------------------------ -| DataDistrib 0.07 20.04 -| Nonbond 0.12 35.83 -| Bond 0.00 0.15 -| Angle 0.00 1.17 -| Dihedral 0.01 4.33 -| Shake 0.00 0.29 -| RunMD 0.13 37.81 -| Other 0.00 0.37 +| DataDistrib 0.01 6.39 +| Nonbond 0.14 67.92 +| Bond 0.00 0.00 +| Angle 0.00 1.00 +| Dihedral 0.01 6.14 +| Shake 0.00 0.63 +| RunMD 0.03 17.29 +| Other 0.00 0.63 | ------------------------------ -| Total 0.34 +| Total 0.20 | Generalized Born CPU Time, Average for All Tasks: | | Routine Sec % | ------------------------------------ -| Radii Calc 0.01 3.16 -| Diagonal Calc 0.03 9.54 -| Off Diagonal Calc 0.02 4.99 -| GBSA LCPO Calc 0.05 15.71 -| Radii Distrib 0.01 1.98 +| Radii Calc 0.02 11.40 +| Diagonal Calc 0.03 15.41 +| Off Diagonal Calc 0.03 13.16 +| GBSA LCPO Calc 0.04 21.68 +| Radii Distrib 0.01 5.89 | --------------------------------- -| Total 0.07 19.68 +| Total 0.09 45.86 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 450 steps: -| Elapsed(s) = 0.31 Per Step(ms) = 0.68 -| ns/day = 254.50 seconds/ns = 339.49 +| Elapsed(s) = 0.18 Per Step(ms) = 0.39 +| ns/day = 439.03 seconds/ns = 196.80 | | Average timings for all steps: -| Elapsed(s) = 0.34 Per Step(ms) = 0.68 -| ns/day = 253.02 seconds/ns = 341.47 +| Elapsed(s) = 0.20 Per Step(ms) = 0.40 +| ns/day = 430.98 seconds/ns = 200.47 | ----------------------------------------------------- | Master Setup CPU time: 0.01 seconds -| Master NonSetup CPU time: 0.34 seconds -| Master Total CPU time: 0.35 seconds 0.00 hours +| Master NonSetup CPU time: 0.20 seconds +| Master Total CPU time: 0.21 seconds 0.00 hours | Master Setup wall time: 0 seconds | Master NonSetup wall time: 0 seconds diff --git test/nfe/smd2/save.sander/mdout test/nfe/smd2/save.sander/mdout index d9b985db98..1b13532208 100644 --- test/nfe/smd2/save.sander/mdout +++ test/nfe/smd2/save.sander/mdout @@ -1,13 +1,13 @@ ------------------------------------------------------- - Amber 16 SANDER 2016 + Amber 18 SANDER 2018 ------------------------------------------------------- -| Run on 06/10/2016 at 16:59:19 +| Run on 09/04/2018 at 09:26:23 -| Executable path: /home/feng/git_feng/amber/bin/sander -| Working directory: /home/feng/git_feng/amber/test/nfe/smd2 -| Hostname: kili.physics.ncsu.edu +| Executable path: /home/feng/local/amber18_patch/bin/sander.MPI +| Working directory: /home/feng/local/amber18_patch/test/nfe/smd2 +| Hostname: gaia.physics.ncsu.edu [-O]verwriting output @@ -28,6 +28,14 @@ File Assignments: |RSTDIP: rstdip |INPTRA: inptraj +| REMLOG: rem.log +| REMTYPE: rem.type +| REMSTRIP: +| SAVEENE: saveene +|CLUSTERINF: cluster.info +| RESERVOIR: reserv/frame +| REMDDIM: + Here is the input file: @@ -37,7 +45,7 @@ File Assignments: irest = 1, ntx = 5, ntc = 2, ntf = 2, tol = 0.000001, ioutfm = 1, igb = 2, gbsa = 1, dt = 0.002, ntpr = 50, ntwx = 0, ntwr = 500, nstlim = 500, - ig = 29166, ntr = 0, nscm = 5000, infe = 1, + ig = 29166, ntr = 0, nscm = 5000, infe = 1, / &smd @@ -50,7 +58,7 @@ File Assignments: 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: +| Flags: MPI | New format PARM file being parsed. | Version = 1.000 Date = 12/14/09 Time = 14:08:03 NATOM = 82 NTYPES = 7 NBONH = 42 MBONA = 44 @@ -64,13 +72,13 @@ File Assignments: Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) | Memory Use Allocated -| Real 9424 +| Real 9710 | Hollerith 255 | Integer 28266 | Max Pairs 1 | nblistReal 0 | nblist Int 0 -| Total 185 kbytes +| Total 187 kbytes | Warning: ATOMIC_NUMBER section not found | Guessing atomic numbers from masses for GB parameters | Remake topology file with AmberTools 12 or add ATOMIC_NUMBERS @@ -124,6 +132,9 @@ Langevin dynamics temperature regulation: SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 + +| MPI Timing options: +| profile_mpi = 0 | INFO: Old style inpcrd file read @@ -135,6 +146,10 @@ ACE begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 +| Atom division among processors: +| 0 20 48 62 82 +| Running AMBER/MPI version on 4 nodes + -------------------------------------------------------------------------------- 4. RESULTS @@ -167,104 +182,145 @@ ACE | TOTAL # of degrees of freedom (RNDF) = 204. NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 275.94 PRESS = 0.0 - Etot = 167.4983 EKtot = 55.9319 EPtot = 111.5664 + Etot = 169.1572 EKtot = 55.9319 EPtot = 113.2252 BOND = 15.8568 ANGLE = 52.2629 DIHED = 86.8661 1-4 NB = 16.2049 1-4 EEL = 287.9575 VDWAALS = -10.9421 - EELEC = -291.1708 EGB = -49.0562 RESTRAINT = 0.0000 + EELEC = -291.1708 EGB = -49.0562 RESTRAINT = 1.6588 ESURF= 3.5873 + EAMBER (non-restraint) = 111.5664 ------------------------------------------------------------------------------ + NFE restraints: SMD : 1.659 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 288.45 PRESS = 0.0 - Etot = 170.7038 EKtot = 58.4669 EPtot = 112.2370 + Etot = 175.4897 EKtot = 58.4669 EPtot = 117.0229 BOND = 14.4795 ANGLE = 60.0408 DIHED = 85.7967 1-4 NB = 14.1420 1-4 EEL = 282.7831 VDWAALS = -11.3633 - EELEC = -290.0343 EGB = -47.1461 RESTRAINT = 0.0000 + EELEC = -290.0343 EGB = -47.1461 RESTRAINT = 4.7859 ESURF= 3.5386 + EAMBER (non-restraint) = 112.2370 ------------------------------------------------------------------------------ + NFE restraints: SMD : 4.786 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 150 TIME(PS) = 0.300 TEMP(K) = 289.60 PRESS = 0.0 - Etot = 177.4099 EKtot = 58.7009 EPtot = 118.7090 + Etot = 179.8021 EKtot = 58.7009 EPtot = 121.1011 BOND = 13.9542 ANGLE = 52.9962 DIHED = 105.0150 1-4 NB = 12.6748 1-4 EEL = 282.4215 VDWAALS = -15.5026 - EELEC = -290.6914 EGB = -45.6790 RESTRAINT = 0.0000 + EELEC = -290.6914 EGB = -45.6790 RESTRAINT = 2.3922 ESURF= 3.5203 + EAMBER (non-restraint) = 118.7090 ------------------------------------------------------------------------------ + NFE restraints: SMD : 2.392 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 200 TIME(PS) = 0.400 TEMP(K) = 302.89 PRESS = 0.0 - Etot = 180.9301 EKtot = 61.3929 EPtot = 119.5372 + Etot = 183.7139 EKtot = 61.3929 EPtot = 122.3210 BOND = 16.5717 ANGLE = 47.3139 DIHED = 107.4803 1-4 NB = 14.8982 1-4 EEL = 286.3698 VDWAALS = -16.9853 - EELEC = -293.6555 EGB = -45.9481 RESTRAINT = 0.0000 + EELEC = -293.6555 EGB = -45.9481 RESTRAINT = 2.7837 ESURF= 3.4923 + EAMBER (non-restraint) = 119.5372 ------------------------------------------------------------------------------ + NFE restraints: SMD : 2.784 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 250 TIME(PS) = 0.500 TEMP(K) = 260.88 PRESS = 0.0 - Etot = 187.1558 EKtot = 52.8786 EPtot = 134.2772 + Etot = 187.9272 EKtot = 52.8786 EPtot = 135.0486 BOND = 17.1069 ANGLE = 62.2403 DIHED = 104.7649 1-4 NB = 15.0971 1-4 EEL = 289.5548 VDWAALS = -16.7702 - EELEC = -297.1551 EGB = -44.0727 RESTRAINT = 0.0000 + EELEC = -297.1551 EGB = -44.0727 RESTRAINT = 0.7714 ESURF= 3.5113 + EAMBER (non-restraint) = 134.2772 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.771 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 300 TIME(PS) = 0.600 TEMP(K) = 282.22 PRESS = 0.0 - Etot = 184.4709 EKtot = 57.2035 EPtot = 127.2675 + Etot = 184.5451 EKtot = 57.2035 EPtot = 127.3416 BOND = 17.2748 ANGLE = 55.5762 DIHED = 107.2426 1-4 NB = 12.2918 1-4 EEL = 286.0311 VDWAALS = -15.5175 - EELEC = -294.7725 EGB = -44.3639 RESTRAINT = 0.0000 + EELEC = -294.7725 EGB = -44.3639 RESTRAINT = 0.0742 ESURF= 3.5049 + EAMBER (non-restraint) = 127.2675 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.074 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 350 TIME(PS) = 0.700 TEMP(K) = 330.80 PRESS = 0.0 - Etot = 182.3983 EKtot = 67.0512 EPtot = 115.3471 + Etot = 184.0704 EKtot = 67.0512 EPtot = 117.0192 BOND = 12.9716 ANGLE = 51.7927 DIHED = 101.1596 1-4 NB = 13.2004 1-4 EEL = 285.4573 VDWAALS = -15.7416 - EELEC = -293.3998 EGB = -43.6556 RESTRAINT = 0.0000 + EELEC = -293.3998 EGB = -43.6556 RESTRAINT = 1.6721 ESURF= 3.5624 + EAMBER (non-restraint) = 115.3471 ------------------------------------------------------------------------------ + NFE restraints: SMD : 1.672 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = 306.12 PRESS = 0.0 - Etot = 179.5992 EKtot = 62.0495 EPtot = 117.5497 + Etot = 179.7182 EKtot = 62.0495 EPtot = 117.6688 BOND = 17.3184 ANGLE = 50.0925 DIHED = 100.9027 1-4 NB = 14.3564 1-4 EEL = 283.5260 VDWAALS = -14.9441 - EELEC = -294.6974 EGB = -42.5575 RESTRAINT = 0.0000 + EELEC = -294.6974 EGB = -42.5575 RESTRAINT = 0.1191 ESURF= 3.5529 + EAMBER (non-restraint) = 117.5497 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.119 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 450 TIME(PS) = 0.900 TEMP(K) = 278.28 PRESS = 0.0 - Etot = 170.9088 EKtot = 56.4060 EPtot = 114.5028 + Etot = 172.4252 EKtot = 56.4060 EPtot = 116.0192 BOND = 19.9606 ANGLE = 61.7312 DIHED = 83.1469 1-4 NB = 12.8673 1-4 EEL = 281.1143 VDWAALS = -13.5707 - EELEC = -291.4499 EGB = -42.8847 RESTRAINT = 0.0000 + EELEC = -291.4499 EGB = -42.8847 RESTRAINT = 1.5164 ESURF= 3.5877 + EAMBER (non-restraint) = 114.5028 ------------------------------------------------------------------------------ + NFE restraints: SMD : 1.516 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 274.14 PRESS = 0.0 - Etot = 170.0523 EKtot = 55.5658 EPtot = 114.4865 + Etot = 170.0691 EKtot = 55.5658 EPtot = 114.5033 BOND = 9.9899 ANGLE = 60.6437 DIHED = 86.9794 1-4 NB = 17.4990 1-4 EEL = 282.7687 VDWAALS = -11.7593 - EELEC = -292.4142 EGB = -42.8089 RESTRAINT = 0.0000 + EELEC = -292.4142 EGB = -42.8089 RESTRAINT = 0.0168 ESURF= 3.5882 + EAMBER (non-restraint) = 114.4865 ------------------------------------------------------------------------------ + NFE restraints: SMD : 0.017 PMD : 0.000 ABMD : 0.000 + BBMD : 0.000 STSM : 0.000 +=============================================================================== A V E R A G E S O V E R 500 S T E P S NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 292.95 PRESS = 0.0 - Etot = 177.0557 EKtot = 59.3793 EPtot = 117.6763 + Etot = 178.8136 EKtot = 59.3793 EPtot = 119.4343 BOND = 15.0505 ANGLE = 55.5629 DIHED = 96.2789 1-4 NB = 14.2424 1-4 EEL = 285.0241 VDWAALS = -14.1785 - EELEC = -292.9692 EGB = -44.8790 RESTRAINT = 0.0000 + EELEC = -292.9692 EGB = -44.8790 RESTRAINT = 1.7579 ESURF= 3.5441 + EAMBER (non-restraint) = 117.6763 ------------------------------------------------------------------------------ @@ -272,11 +328,12 @@ ACE NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 22.14 PRESS = 0.0 - Etot = 7.0222 EKtot = 4.4877 EPtot = 8.2817 + Etot = 7.0276 EKtot = 4.4877 EPtot = 8.2883 BOND = 3.0636 ANGLE = 4.4897 DIHED = 9.1964 1-4 NB = 1.3219 1-4 EEL = 2.0714 VDWAALS = 1.7853 - EELEC = 2.3536 EGB = 2.1545 RESTRAINT = 0.0000 + EELEC = 2.3536 EGB = 2.1545 RESTRAINT = 1.5167 ESURF= 0.0371 + EAMBER (non-restraint) = 6.7717 ------------------------------------------------------------------------------ @@ -284,24 +341,28 @@ ACE 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.00 ( 0.04% of Total) -| Calc gb radii 0.19 (15.48% of Gen B) -| Calc gb diag 0.36 (30.07% of Gen B) -| Calc gb off-diag 0.29 (23.99% of Gen B) -| Surface area energy 0.37 (30.42% of Gen B) -| Other 0.00 ( 0.05% of Gen B) -| Gen Born time 1.21 (100.0% of Nonbo) -| IPS excludes 0.00 ( 0.01% of Nonbo) -| Nonbond force 1.21 (91.39% of Force) -| Bond/Angle/Dihedral 0.10 ( 7.23% of Force) -| Other 0.02 ( 1.38% of Force) -| Force time 1.32 (97.49% of Runmd) -| Shake time 0.00 ( 0.26% of Runmd) -| Verlet update time 0.03 ( 2.12% of Runmd) -| Other 0.00 ( 0.13% of Runmd) -| Runmd Time 1.35 (99.59% of Total) -| Other 0.00 ( 0.36% of Total) -| Total time 1.36 (99.80% of ALL ) +|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> +| Read coords time 0.00 ( 0.08% of Total) +| Calc gb radii 0.03 (16.28% of Gen B) +| Communicate gb radii 0.01 ( 6.71% of Gen B) +| Calc gb diag 0.04 (27.88% of Gen B) +| Calc gb off-diag 0.04 (22.30% of Gen B) +| Surface area energy 0.04 (26.63% of Gen B) +| Other 0.00 ( 0.19% of Gen B) +| Gen Born time 0.16 (100.0% of Nonbo) +| IPS excludes 0.00 ( 0.02% of Nonbo) +| Nonbond force 0.16 (82.24% of Force) +| Bond/Angle/Dihedral 0.01 ( 7.68% of Force) +| FRC Collect time 0.00 ( 1.85% of Force) +| Other 0.02 ( 8.23% of Force) +| Force time 0.19 (89.81% of Runmd) +| Shake time 0.00 ( 0.52% of Runmd) +| Verlet update time 0.02 ( 8.02% of Runmd) +| CRD distribute time 0.00 ( 0.43% of Runmd) +| Other 0.00 ( 1.22% of Runmd) +| Runmd Time 0.22 (95.75% of Total) +| Other 0.01 ( 4.16% of Total) +| Total time 0.23 (99.56% of ALL ) | Number of list builds : 0 @@ -311,11 +372,11 @@ ACE | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: -| Elapsed(s) = 1.35 Per Step(ms) = 2.71 -| ns/day = 63.81 seconds/ns = 1353.94 +| Elapsed(s) = 0.22 Per Step(ms) = 0.43 +| ns/day = 397.87 seconds/ns = 217.16 | ----------------------------------------------------- -| Job began at 16:59:19.684 on 06/10/2016 -| Setup done at 16:59:19.693 on 06/10/2016 -| Run done at 16:59:21.046 on 06/10/2016 -| wallclock() was called 13023 times +| Job began at 09:26:23.427 on 09/04/2018 +| Setup done at 09:26:23.438 on 09/04/2018 +| Run done at 09:26:23.655 on 09/04/2018 +| wallclock() was called 18523 times