------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 14 | Run on 03/29/2017 at 17:44:35 | Executable path: /home/softadmin/SOFTWARE_INSTALL/amber14/bin/pmemd.cuda | Working directory: /scratch2/sramsey.1360.master.lehman.edu | Hostname: node9 [-O]verwriting output File Assignments: | MDIN: md-heat-50K.in | MDOUT: heat1.out | INPCRD: min_fxa-2.rst7 | PARM: fxa.prmtop | RESTRT: md_heat-50K.rst7 | REFC: min_fxa-2.rst7 | MDVEL: mdvel | MDEN: mden | MDCRD: heat1.nc | MDINFO: mdinfo | MDFRC: mdfrc Here is the input file: Heating run with increment of 50 K each for 200ps &cntrl imin = 0, irest = 0, ntx = 1, ntb = 1, ntc = 2, ntf = 2, cut = 9.0, tempi = 0.0, temp0 = 50.0, ntt = 3, gamma_ln = 2.0, nstlim = 10000, dt = 0.002, iwrap = 1, ntpr = 1000, ntwx = 1000, ntwr = 10000, nscm = 1000, ntr=1, restraint_wt=100, restraintmask='!:WAT & !@H', ig=-1, ioutfm=1, &end Note: ig = -1. Setting random seed to 689912 based on wallclock time in microseconds. |--------------------- INFORMATION ---------------------- | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE. | Version 14.0.1 | | 06/20/2014 | | Implementation by: | Ross C. Walker (SDSC) | Scott Le Grand (nVIDIA) | | CAUTION: The CUDA code is currently experimental. | You use it at your own risk. Be sure to | check ALL results carefully. | | Precision model in use: | [SPFP] - Mixed Single/Double/Fixed Point Precision. | (Default) | |-------------------------------------------------------- |----------------- CITATION INFORMATION ----------------- | | When publishing work that utilized the CUDA version | of AMBER, please cite the following in addition to | the regular AMBER citations: | | - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan | Poole; Scott Le Grand; Ross C. Walker "Routine | microsecond molecular dynamics simulations with | AMBER - Part II: Particle Mesh Ewald", J. Chem. | Theory Comput., 2013, 9 (9), pp3878-3888, | DOI: 10.1021/ct400314y. | | - Andreas W. Goetz; Mark J. Williamson; Dong Xu; | Duncan Poole; Scott Le Grand; Ross C. Walker | "Routine microsecond molecular dynamics simulations | with AMBER - Part I: Generalized Born", J. Chem. | Theory Comput., 2012, 8 (5), pp1542-1555. | | - Scott Le Grand; Andreas W. Goetz; Ross C. Walker | "SPFP: Speed without compromise - a mixed precision | model for GPU accelerated molecular dynamics | simulations.", Comp. Phys. Comm., 2013, 184 | pp374-380, DOI: 10.1016/j.cpc.2012.09.022 | |-------------------------------------------------------- |------------------- GPU DEVICE INFO -------------------- | | CUDA_VISIBLE_DEVICES: not set | CUDA Capable Devices Detected: 8 | CUDA Device ID in use: 0 | CUDA Device Name: GeForce GTX 980 | CUDA Device Global Mem Size: 4095 MB | CUDA Device Num Multiprocessors: 16 | CUDA Device Core Freq: 1.27 GHz | |-------------------------------------------------------- | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | CUDA | EMIL | Largest sphere to fit in unit cell has radius = 33.886 | New format PARM file being parsed. | Version = 1.000 Date = 03/29/17 Time = 10:16:47 | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 30021 NTYPES = 16 NBONH = 28164 MBONA = 1895 NTHETH = 4135 MTHETA = 2553 NPHIH = 8468 MPHIA = 8019 NHPARM = 0 NPARM = 0 NNB = 55343 NRES = 9018 NBONA = 1895 NTHETA = 2553 NPHIA = 8019 NUMBND = 66 NUMANG = 154 NPTRA = 202 NATYP = 35 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 14 15 13 | Direct force subcell size = 5.1810 5.2423 5.2132 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 10000 iwrap = 1, ntwx = 1000, 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 = 9.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 1 restraint_wt = 100.00000 Molecular dynamics: nstlim = 10000, nscm = 0, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = -1.00000 Langevin dynamics temperature regulation: ig = 689912 temp0 = 50.00000, tempi = 0.00000, gamma_ln= 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 72.535 Box Y = 78.634 Box Z = 67.771 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 80 NFFT2 = 80 NFFT3 = 64 Cutoff= 9.000 Tol =0.100E-04 Ewald Coefficient = 0.30768 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES default_name Mask !:WAT & !@H; matches 3446 atoms -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 8782 Sum of charges from parm topology file = 1.99999989 Assuming uniform neutralizing plasma | Dynamic Memory, Types Used: | Reals 1007469 | Integers 1101562 | Nonbonded Pairs Initial Allocation: 6844788 | GPU memory information (estimate): | KB of GPU memory in use: 177713 | KB of CPU memory in use: 38177 -------------------------------------------------------------------------------- 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 = 0.8314E-11 at 2.736960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.39 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.84 |--------------------------------------------------- NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -125344.5965 EKtot = 0.0000 EPtot = -125344.5965 BOND = 135.1219 ANGLE = 472.5394 DIHED = 2581.7134 1-4 NB = 729.0081 1-4 EEL = 9358.3545 VDWAALS = 22459.8207 EELEC = -161081.1545 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 53.47 PRESS = 0.0 Etot = -104286.0335 EKtot = 3288.6067 EPtot = -107574.6402 BOND = 213.5132 ANGLE = 589.6798 DIHED = 2610.7039 1-4 NB = 736.5007 1-4 EEL = 9358.4465 VDWAALS = 18121.6949 EELEC = -139456.7376 EHBOND = 0.0000 RESTRAINT = 251.5586 EAMBER (non-restraint) = -107826.1988 ------------------------------------------------------------------------------ NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 51.17 PRESS = 0.0 Etot = -105389.4351 EKtot = 3147.0574 EPtot = -108536.4925 BOND = 207.9506 ANGLE = 601.8258 DIHED = 2610.3687 1-4 NB = 734.1715 1-4 EEL = 9359.0438 VDWAALS = 18470.9488 EELEC = -140774.3120 EHBOND = 0.0000 RESTRAINT = 253.5103 EAMBER (non-restraint) = -108790.0028 ------------------------------------------------------------------------------ NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 50.01 PRESS = 0.0 Etot = -105808.8560 EKtot = 3075.7449 EPtot = -108884.6009 BOND = 218.9779 ANGLE = 603.5550 DIHED = 2612.9090 1-4 NB = 736.7169 1-4 EEL = 9343.3578 VDWAALS = 18547.9969 EELEC = -141203.7372 EHBOND = 0.0000 RESTRAINT = 255.6228 EAMBER (non-restraint) = -109140.2237 ------------------------------------------------------------------------------ NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 50.19 PRESS = 0.0 Etot = -106024.2222 EKtot = 3086.9194 EPtot = -109111.1416 BOND = 215.2875 ANGLE = 608.8436 DIHED = 2608.1146 1-4 NB = 734.4179 1-4 EEL = 9344.1584 VDWAALS = 18503.5358 EELEC = -141383.2619 EHBOND = 0.0000 RESTRAINT = 257.7625 EAMBER (non-restraint) = -109368.9041 ------------------------------------------------------------------------------ NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 49.92 PRESS = 0.0 Etot = -106173.9375 EKtot = 3070.0530 EPtot = -109243.9905 BOND = 214.7276 ANGLE = 598.2646 DIHED = 2607.0192 1-4 NB = 737.5737 1-4 EEL = 9356.3984 VDWAALS = 18482.7448 EELEC = -141494.5860 EHBOND = 0.0000 RESTRAINT = 253.8672 EAMBER (non-restraint) = -109497.8577 ------------------------------------------------------------------------------ NSTEP = 6000 TIME(PS) = 12.000 TEMP(K) = 50.04 PRESS = 0.0 Etot = -106283.7168 EKtot = 3077.8042 EPtot = -109361.5210 BOND = 220.6115 ANGLE = 597.2931 DIHED = 2602.6497 1-4 NB = 734.1300 1-4 EEL = 9350.2629 VDWAALS = 18689.0010 EELEC = -141805.6896 EHBOND = 0.0000 RESTRAINT = 250.2203 EAMBER (non-restraint) = -109611.7413 ------------------------------------------------------------------------------ NSTEP = 7000 TIME(PS) = 14.000 TEMP(K) = 50.13 PRESS = 0.0 Etot = -106345.8049 EKtot = 3082.9983 EPtot = -109428.8032 BOND = 213.3940 ANGLE = 601.9102 DIHED = 2612.1651 1-4 NB = 734.1688 1-4 EEL = 9365.3078 VDWAALS = 18661.8447 EELEC = -141870.4659 EHBOND = 0.0000 RESTRAINT = 252.8721 EAMBER (non-restraint) = -109681.6753 ------------------------------------------------------------------------------ NSTEP = 8000 TIME(PS) = 16.000 TEMP(K) = 49.83 PRESS = 0.0 Etot = -106431.9133 EKtot = 3064.7754 EPtot = -109496.6887 BOND = 208.2487 ANGLE = 605.9683 DIHED = 2607.0504 1-4 NB = 736.3554 1-4 EEL = 9356.9592 VDWAALS = 18822.0473 EELEC = -142093.6052 EHBOND = 0.0000 RESTRAINT = 260.2872 EAMBER (non-restraint) = -109756.9759 ------------------------------------------------------------------------------ NSTEP = 9000 TIME(PS) = 18.000 TEMP(K) = 50.15 PRESS = 0.0 Etot = -106476.2762 EKtot = 3084.2317 EPtot = -109560.5079 BOND = 213.3672 ANGLE = 596.5243 DIHED = 2607.5123 1-4 NB = 735.4546 1-4 EEL = 9347.1954 VDWAALS = 18630.5575 EELEC = -141943.0684 EHBOND = 0.0000 RESTRAINT = 251.9491 EAMBER (non-restraint) = -109812.4571 ------------------------------------------------------------------------------ NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 49.99 PRESS = 0.0 Etot = -106514.5808 EKtot = 3074.6455 EPtot = -109589.2264 BOND = 218.4999 ANGLE = 604.6000 DIHED = 2607.4843 1-4 NB = 731.2822 1-4 EEL = 9349.5073 VDWAALS = 18748.0686 EELEC = -142108.2995 EHBOND = 0.0000 RESTRAINT = 259.6308 EAMBER (non-restraint) = -109848.8572 ------------------------------------------------------------------------------ A V E R A G E S O V E R 10 S T E P S NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 50.49 PRESS = 0.0 Etot = -105973.4776 EKtot = 3105.2836 EPtot = -109078.7613 BOND = 214.4578 ANGLE = 600.8465 DIHED = 2608.5977 1-4 NB = 735.0772 1-4 EEL = 9353.0638 VDWAALS = 18567.8440 EELEC = -141413.3763 EHBOND = 0.0000 RESTRAINT = 254.7281 EAMBER (non-restraint) = -109333.4894 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 1.05 PRESS = 0.0 Etot = 651.8490 EKtot = 64.8675 EPtot = 590.9554 BOND = 3.9939 ANGLE = 5.2571 DIHED = 2.8601 1-4 NB = 1.7350 1-4 EEL = 6.8512 VDWAALS = 185.6764 EELEC = 766.6376 EHBOND = 0.0000 RESTRAINT = 3.2970 EAMBER (non-restraint) = 587.6584 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 1.06 6.50 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.00 0.00 | Shake 0.09 0.54 | RunMD 15.14 92.85 | Other 0.02 0.11 | ------------------------------ | Total 16.30 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 | Build List 0.00 0.00 | --------------------------------- | Total 0.00 0.00 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.00 0.00 | Exclude Masked 0.00 0.00 | Other 0.01 0.05 | --------------------------------- | Total 0.01 0.05 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.00 0.00 | Grid Charges 0.00 0.00 | Scalar Sum 0.00 0.00 | Gradient Sum 0.00 0.00 | FFT 0.00 0.00 | --------------------------------- | Total 0.00 0.00 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 10000 steps: | Elapsed(s) = 16.30 Per Step(ms) = 1.63 | ns/day = 105.98 seconds/ns = 815.23 | | Average timings for all steps: | Elapsed(s) = 16.30 Per Step(ms) = 1.63 | ns/day = 105.98 seconds/ns = 815.23 | ----------------------------------------------------- | Setup CPU time: 1.14 seconds | NonSetup CPU time: 16.30 seconds | Total CPU time: 17.44 seconds 0.00 hours | Setup wall time: 1 seconds | NonSetup wall time: 16 seconds | Total wall time: 17 seconds 0.00 hours