------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 10/01/2012 at 18:44:52 [-O]verwriting output File Assignments: | MDIN: mdin_min.60 | MDOUT: ala_tri_min_60.out | INPCRD: ala_tri_prod_120.rst | PARM: ala_tri.prmtop | RESTRT: ala_tri_min_60.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo |LOGFILE: logfile Here is the input file: 2000 step minimization for 60 deg &cntrl imin = 1, maxcyc=2000, ncyc = 500, ntpr = 100, ntwr = 1000, ntf = 1, ntc = 1, cut = 8.0, ntb = 1, ntp = 0, nmropt = 1, &end &wt type='END', &end DISANG=disang.60 | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | MPI | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | Largest sphere to fit in unit cell has radius = 13.386 | New format PARM file being parsed. | Version = 1.000 Date = 10/01/12 Time = 16:17:26 | 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 = 2681 NTYPES = 9 NBONH = 2666 MBONA = 14 NTHETH = 36 MTHETA = 18 NPHIH = 64 MPHIA = 45 NHPARM = 0 NPARM = 0 NNB = 3684 NRES = 887 NBONA = 14 NTHETA = 18 NPHIA = 45 NUMBND = 10 NUMANG = 16 NPTRA = 19 NATYP = 9 NPHB = 1 IFBOX = 2 NMXRS = 10 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 5 5 5 | Direct force subcell size = 6.5579 6.5579 6.5579 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- ACE General flags: imin = 1, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 1000 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, 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 Energy minimization: maxcyc = 2000, ncyc = 500, ntmin = 1 dx0 = 0.01000, drms = 0.00010 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 32.790 Box Y = 32.790 Box Z = 32.790 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 -------------------------------------------------------------------------------- ACE begin time read from input coords = 150.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: ** No weight changes given ** RESTRAINTS: Requested file redirections: DISANG = disang.60 Restraints will be read from file: disang.60 Here are comments from the DISANG input file: Number of restraints read = 1 Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 883 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 222836 | Integers 176453 | Nonbonded Pairs Initial Allocation: 305634 | Running AMBER/MPI version on 2 nodes -------------------------------------------------------------------------------- 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 |--------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 -8.2706E+03 1.6782E+01 4.2275E+02 N 17 BOND = 5.0948 ANGLE = 14.4371 DIHED = 24.5131 VDWAALS = 1246.7097 EEL = -9957.7346 HBOND = 0.0000 1-4 VDW = 5.1986 1-4 EEL = 117.7777 RESTRAINT = 273.3972 EAMBER = -8544.0036 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 273.397 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.0139E+04 2.9845E+00 1.4679E+02 C 15 BOND = 663.2367 ANGLE = 41.1857 DIHED = 38.3673 VDWAALS = 1121.7537 EEL = -12119.1091 HBOND = 0.0000 1-4 VDW = 4.8527 1-4 EEL = 111.1372 RESTRAINT = 0.0007 EAMBER = -10138.5758 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.001 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.0404E+04 2.3875E+00 1.1563E+02 C 15 BOND = 695.3168 ANGLE = 21.1429 DIHED = 37.5623 VDWAALS = 1202.4689 EEL = -12486.9288 HBOND = 0.0000 1-4 VDW = 4.6649 1-4 EEL = 110.5979 RESTRAINT = 11.1743 EAMBER = -10415.1751 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 11.174 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.0548E+04 2.1450E+00 1.0476E+02 C 15 BOND = 714.9552 ANGLE = 28.5106 DIHED = 38.9790 VDWAALS = 1279.5137 EEL = -12724.4178 HBOND = 0.0000 1-4 VDW = 4.4563 1-4 EEL = 110.2165 RESTRAINT = 0.0427 EAMBER = -10547.7865 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.043 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 400 -1.0653E+04 4.6767E-01 5.0239E+00 C 15 BOND = 731.7033 ANGLE = 20.8912 DIHED = 38.8750 VDWAALS = 1349.4060 EEL = -12908.6597 HBOND = 0.0000 1-4 VDW = 4.3874 1-4 EEL = 109.7255 RESTRAINT = 1.1711 EAMBER = -10653.6712 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.171 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 500 -1.0731E+04 1.4572E+00 6.8737E+01 C 15 BOND = 746.1827 ANGLE = 21.2976 DIHED = 37.4932 VDWAALS = 1413.0560 EEL = -13061.8935 HBOND = 0.0000 1-4 VDW = 4.2512 1-4 EEL = 108.1638 RESTRAINT = 0.0105 EAMBER = -10731.4490 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.010 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 600 -1.1033E+04 7.7032E-01 2.9010E+01 N 17 BOND = 815.1873 ANGLE = 12.5470 DIHED = 33.5020 VDWAALS = 1742.1548 EEL = -13749.7746 HBOND = 0.0000 1-4 VDW = 4.3144 1-4 EEL = 108.5653 RESTRAINT = 0.5843 EAMBER = -11033.5038 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.584 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 700 -1.1117E+04 5.0865E-01 1.8955E+01 N 17 BOND = 832.6292 ANGLE = 10.4168 DIHED = 32.0235 VDWAALS = 1828.2403 EEL = -13933.9666 HBOND = 0.0000 1-4 VDW = 4.2989 1-4 EEL = 108.8823 RESTRAINT = 0.3169 EAMBER = -11117.4756 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.317 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 800 -1.1180E+04 4.7753E-01 1.0760E+01 CA 9 BOND = 846.3196 ANGLE = 9.3966 DIHED = 31.3942 VDWAALS = 1888.7250 EEL = -14069.6621 HBOND = 0.0000 1-4 VDW = 4.3479 1-4 EEL = 109.1102 RESTRAINT = 0.1518 EAMBER = -11180.3687 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.152 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 900 -1.1227E+04 4.2822E-01 9.6140E+00 CA 9 BOND = 856.3736 ANGLE = 8.6399 DIHED = 31.3019 VDWAALS = 1937.5118 EEL = -14174.7648 HBOND = 0.0000 1-4 VDW = 4.3293 1-4 EEL = 109.1566 RESTRAINT = 0.1386 EAMBER = -11227.4517 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.139 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -1.1274E+04 3.4534E-01 1.0748E+01 C 15 BOND = 867.0174 ANGLE = 7.3812 DIHED = 31.3503 VDWAALS = 1992.0833 EEL = -14285.6823 HBOND = 0.0000 1-4 VDW = 4.2920 1-4 EEL = 109.4399 RESTRAINT = 0.2317 EAMBER = -11274.1182 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.232 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1100 -1.1306E+04 2.9550E-01 6.1266E+00 C 5 BOND = 874.9138 ANGLE = 7.3768 DIHED = 30.9940 VDWAALS = 2026.6003 EEL = -14359.1548 HBOND = 0.0000 1-4 VDW = 4.2923 1-4 EEL = 109.3599 RESTRAINT = 0.1114 EAMBER = -11305.6177 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.111 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1200 -1.1329E+04 1.9503E-01 3.7058E+00 N 27 BOND = 879.8716 ANGLE = 7.0525 DIHED = 30.8756 VDWAALS = 2052.3899 EEL = -14413.0325 HBOND = 0.0000 1-4 VDW = 4.3555 1-4 EEL = 109.5849 RESTRAINT = 0.1179 EAMBER = -11328.9025 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.118 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1300 -1.1353E+04 2.1454E-01 3.5271E+00 C 25 BOND = 885.2369 ANGLE = 6.8230 DIHED = 30.7105 VDWAALS = 2081.8745 EEL = -14471.5952 HBOND = 0.0000 1-4 VDW = 4.4149 1-4 EEL = 109.7338 RESTRAINT = 0.0797 EAMBER = -11352.8015 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.080 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1400 -1.1366E+04 1.2531E-01 3.1441E+00 C 5 BOND = 891.4359 ANGLE = 6.5539 DIHED = 30.5454 VDWAALS = 2104.1428 EEL = -14513.0581 HBOND = 0.0000 1-4 VDW = 4.4680 1-4 EEL = 109.8559 RESTRAINT = 0.0608 EAMBER = -11366.0561 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.061 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1500 -1.1377E+04 2.2813E-01 8.2118E+00 C 15 BOND = 894.5381 ANGLE = 6.5834 DIHED = 30.4047 VDWAALS = 2122.4679 EEL = -14545.8350 HBOND = 0.0000 1-4 VDW = 4.4952 1-4 EEL = 110.0064 RESTRAINT = 0.0082 EAMBER = -11377.3392 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.008 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1600 -1.1389E+04 8.9309E-02 1.5187E+00 HH33 32 BOND = 897.8777 ANGLE = 6.4423 DIHED = 30.2895 VDWAALS = 2141.6440 EEL = -14579.3866 HBOND = 0.0000 1-4 VDW = 4.5011 1-4 EEL = 110.0362 RESTRAINT = 0.0391 EAMBER = -11388.5960 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.039 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1700 -1.1394E+04 8.8732E-02 2.0102E+00 O 26 BOND = 898.9595 ANGLE = 6.3043 DIHED = 30.2679 VDWAALS = 2147.3603 EEL = -14591.7695 HBOND = 0.0000 1-4 VDW = 4.5707 1-4 EEL = 110.3161 RESTRAINT = 0.0484 EAMBER = -11393.9908 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.048 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1800 -1.1402E+04 8.2932E-02 1.3285E+00 CA 19 BOND = 900.6925 ANGLE = 6.3124 DIHED = 30.1629 VDWAALS = 2151.7441 EEL = -14606.0561 HBOND = 0.0000 1-4 VDW = 4.5397 1-4 EEL = 110.2423 RESTRAINT = 0.0376 EAMBER = -11402.3622 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.038 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 1900 -1.1410E+04 8.8228E-02 1.7905E+00 CA 19 BOND = 903.6209 ANGLE = 6.2562 DIHED = 30.1300 VDWAALS = 2164.0006 EEL = -14628.4581 HBOND = 0.0000 1-4 VDW = 4.5016 1-4 EEL = 110.1724 RESTRAINT = 0.0277 EAMBER = -11409.7765 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.028 =============================================================================== NSTEP ENERGY RMS GMAX NAME NUMBER 2000 -1.1417E+04 2.5777E-01 4.7607E+00 CH3 29 BOND = 905.8108 ANGLE = 6.3557 DIHED = 30.5143 VDWAALS = 2175.1997 EEL = -14649.2569 HBOND = 0.0000 1-4 VDW = 4.2016 1-4 EEL = 110.1091 RESTRAINT = 0.0578 EAMBER = -11417.0658 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.058 =============================================================================== Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 2000 -1.1417E+04 2.5777E-01 4.7607E+00 CH3 29 BOND = 905.8108 ANGLE = 6.3557 DIHED = 30.5143 VDWAALS = 2175.1997 EEL = -14649.2569 HBOND = 0.0000 1-4 VDW = 4.2016 1-4 EEL = 110.1091 RESTRAINT = 0.0578 EAMBER = -11417.0658 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.058 =============================================================================== -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ | DataDistrib 0.58 2.41 | Nonbond 23.28 96.84 | Bond 0.07 0.29 | Angle 0.03 0.10 | Dihedral 0.01 0.04 | Shake 0.00 0.00 | Other 0.07 0.31 | ------------------------------ | Total 24.03 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | Set Up Cit 0.01 0.02 | Build List 0.88 3.66 | --------------------------------- | Total 0.88 3.68 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | NonBonded Calc 15.65 65.09 | Exclude Masked 0.13 0.56 | Other 0.17 0.73 | --------------------------------- | Total 15.95 66.38 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | 1D bspline 0.25 1.04 | Grid Charges 0.30 1.27 | Scalar Sum 2.02 8.43 | Gradient Sum 0.39 1.62 | FFT 3.43 14.25 | --------------------------------- | Total 6.40 26.61 | 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 1 steps: | Elapsed(s) = 24.09 Per Step(ms) = 24090.27 | ns/day = 0.00 seconds/ns = ********** | | Average timings for all steps: | Elapsed(s) = 24.09 Per Step(ms) = 24090.27 | ns/day = 0.00 seconds/ns = ********** | ----------------------------------------------------- | Master Setup CPU time: 0.04 seconds | Master NonSetup CPU time: 24.03 seconds | Master Total CPU time: 24.07 seconds 0.01 hours | Master Setup wall time: 0 seconds | Master NonSetup wall time: 24 seconds | Master Total wall time: 24 seconds 0.01 hours