SHARE
TWEET

gromacs-lysozyme

mahmoodn Feb 28th, 2018 99 Never
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
  1. Log file opened on Wed Feb 28 19:23:23 2018
  2. Host: orca  pid: 3773  rank ID: 0  number of ranks:  1
  3.                        :-) GROMACS - gmx mdrun, 2018 (-:
  4.  
  5.                             GROMACS is written by:
  6.      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar  
  7.  Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  
  8.  Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
  9.     Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  10.   Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff
  11.    Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk  
  12.    Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  
  13.    Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf  
  14.                            and the project leaders:
  15.         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
  16.  
  17. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  18. Copyright (c) 2001-2017, The GROMACS development team at
  19. Uppsala University, Stockholm University and
  20. the Royal Institute of Technology, Sweden.
  21. check out http://www.gromacs.org for more information.
  22.  
  23. GROMACS is free software; you can redistribute it and/or modify it
  24. under the terms of the GNU Lesser General Public License
  25. as published by the Free Software Foundation; either version 2.1
  26. of the License, or (at your option) any later version.
  27.  
  28. GROMACS:      gmx mdrun, version 2018
  29. Executable:   /usr/local/gromacs/bin/gmx
  30. Data prefix:  /usr/local/gromacs
  31. Working dir:  /home/mahmood/gromacs-2018/bench/lysozyme
  32. Command line:
  33.   gmx mdrun -nobackup -nb gpu -deffnm md_0_1
  34.  
  35. GROMACS version:    2018
  36. Precision:          single
  37. Memory model:       64 bit
  38. MPI library:        thread_mpi
  39. OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
  40. GPU support:        CUDA
  41. SIMD instructions:  AVX2_128
  42. FFT library:        fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
  43. RDTSCP usage:       enabled
  44. TNG support:        enabled
  45. Hwloc support:      disabled
  46. Tracing support:    disabled
  47. Built on:           2018-02-23 17:10:06
  48. Built by:           mahmood@orca [CMAKE]
  49. Build OS/arch:      Linux 4.10.0-28-generic x86_64
  50. Build CPU vendor:   AMD
  51. Build CPU brand:    AMD Ryzen 7 1800X Eight-Core Processor
  52. Build CPU family:   23   Model: 1   Stepping: 1
  53. Build CPU features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
  54. C compiler:         /usr/bin/cc GNU 5.4.0
  55. C compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
  56. C++ compiler:       /usr/bin/c++ GNU 5.4.0
  57. C++ compiler flags:  -march=core-avx2    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
  58. CUDA compiler:      /usr/local/cuda-9.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2017 NVIDIA Corporation;Built on Fri_Sep__1_21:08:03_CDT_2017;Cuda compilation tools, release 9.0, V9.0.176
  59. CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;-D_FORCE_INLINES;; ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
  60. CUDA driver:        9.0
  61. CUDA runtime:       9.0
  62.  
  63.  
  64. Running on 1 node with total 16 cores, 16 logical cores, 1 compatible GPU
  65. Hardware detected:
  66.   CPU info:
  67.     Vendor: AMD
  68.     Brand:  AMD Ryzen 7 1800X Eight-Core Processor        
  69.     Family: 23   Model: 1   Stepping: 1
  70.     Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
  71.   Hardware topology: Basic
  72.     Sockets, cores, and logical processors:
  73.       Socket  0: [   0] [   1] [   2] [   3] [   4] [   5] [   6] [   7] [   8] [   9] [  10] [  11] [  12] [  13] [  14] [  15]
  74.   GPU info:
  75.     Number of GPUs detected: 1
  76.     #0: NVIDIA Quadro M2000, compute cap.: 5.2, ECC:  no, stat: compatible
  77.  
  78.  
  79. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  80. M. J. Abraham, T. Murtola, R. Schulz, S. PƔll, J. C. Smith, B. Hess, E.
  81. Lindahl
  82. GROMACS: High performance molecular simulations through multi-level
  83. parallelism from laptops to supercomputers
  84. SoftwareX 1 (2015) pp. 19-25
  85. -------- -------- --- Thank You --- -------- --------
  86.  
  87.  
  88. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  89. S. PƔll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
  90. Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
  91. GROMACS
  92. In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
  93. -------- -------- --- Thank You --- -------- --------
  94.  
  95.  
  96. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  97. S. Pronk, S. PƔll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
  98. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
  99. GROMACS 4.5: a high-throughput and highly parallel open source molecular
  100. simulation toolkit
  101. Bioinformatics 29 (2013) pp. 845-54
  102. -------- -------- --- Thank You --- -------- --------
  103.  
  104.  
  105. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  106. B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
  107. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
  108. molecular simulation
  109. J. Chem. Theory Comput. 4 (2008) pp. 435-447
  110. -------- -------- --- Thank You --- -------- --------
  111.  
  112.  
  113. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  114. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
  115. Berendsen
  116. GROMACS: Fast, Flexible and Free
  117. J. Comp. Chem. 26 (2005) pp. 1701-1719
  118. -------- -------- --- Thank You --- -------- --------
  119.  
  120.  
  121. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  122. E. Lindahl and B. Hess and D. van der Spoel
  123. GROMACS 3.0: A package for molecular simulation and trajectory analysis
  124. J. Mol. Mod. 7 (2001) pp. 306-317
  125. -------- -------- --- Thank You --- -------- --------
  126.  
  127.  
  128. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  129. H. J. C. Berendsen, D. van der Spoel and R. van Drunen
  130. GROMACS: A message-passing parallel molecular dynamics implementation
  131. Comp. Phys. Comm. 91 (1995) pp. 43-56
  132. -------- -------- --- Thank You --- -------- --------
  133.  
  134. Input Parameters:
  135.    integrator                     = md
  136.    tinit                          = 0
  137.    dt                             = 0.002
  138.    nsteps                         = 50000
  139.    init-step                      = 0
  140.    simulation-part                = 1
  141.    comm-mode                      = Linear
  142.    nstcomm                        = 100
  143.    bd-fric                        = 0
  144.    ld-seed                        = -1283751987
  145.    emtol                          = 10
  146.    emstep                         = 0.01
  147.    niter                          = 20
  148.    fcstep                         = 0
  149.    nstcgsteep                     = 1000
  150.    nbfgscorr                      = 10
  151.    rtpi                           = 0.05
  152.    nstxout                        = 5000
  153.    nstvout                        = 5000
  154.    nstfout                        = 0
  155.    nstlog                         = 5000
  156.    nstcalcenergy                  = 100
  157.    nstenergy                      = 5000
  158.    nstxout-compressed             = 5000
  159.    compressed-x-precision         = 1000
  160.    cutoff-scheme                  = Verlet
  161.    nstlist                        = 10
  162.    ns-type                        = Grid
  163.    pbc                            = xyz
  164.    periodic-molecules             = false
  165.    verlet-buffer-tolerance        = 0.005
  166.    rlist                          = 1
  167.    coulombtype                    = PME
  168.    coulomb-modifier               = Potential-shift
  169.    rcoulomb-switch                = 0
  170.    rcoulomb                       = 1
  171.    epsilon-r                      = 1
  172.    epsilon-rf                     = inf
  173.    vdw-type                       = Cut-off
  174.    vdw-modifier                   = Potential-shift
  175.    rvdw-switch                    = 0
  176.    rvdw                           = 1
  177.    DispCorr                       = EnerPres
  178.    table-extension                = 1
  179.    fourierspacing                 = 0.16
  180.    fourier-nx                     = 44
  181.    fourier-ny                     = 44
  182.    fourier-nz                     = 44
  183.    pme-order                      = 4
  184.    ewald-rtol                     = 1e-05
  185.    ewald-rtol-lj                  = 0.001
  186.    lj-pme-comb-rule               = Geometric
  187.    ewald-geometry                 = 0
  188.    epsilon-surface                = 0
  189.    implicit-solvent               = No
  190.    gb-algorithm                   = Still
  191.    nstgbradii                     = 1
  192.    rgbradii                       = 1
  193.    gb-epsilon-solvent             = 80
  194.    gb-saltconc                    = 0
  195.    gb-obc-alpha                   = 1
  196.    gb-obc-beta                    = 0.8
  197.    gb-obc-gamma                   = 4.85
  198.    gb-dielectric-offset           = 0.009
  199.    sa-algorithm                   = Ace-approximation
  200.    sa-surface-tension             = 2.05016
  201.    tcoupl                         = V-rescale
  202.    nsttcouple                     = 10
  203.    nh-chain-length                = 0
  204.    print-nose-hoover-chain-variables = false
  205.    pcoupl                         = Parrinello-Rahman
  206.    pcoupltype                     = Isotropic
  207.    nstpcouple                     = 10
  208.    tau-p                          = 4
  209.    compressibility (3x3):
  210.       compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
  211.       compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
  212.       compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
  213.    ref-p (3x3):
  214.       ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
  215.       ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
  216.       ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
  217.    refcoord-scaling               = No
  218.    posres-com (3):
  219.       posres-com[0]= 0.00000e+00
  220.       posres-com[1]= 0.00000e+00
  221.       posres-com[2]= 0.00000e+00
  222.    posres-comB (3):
  223.       posres-comB[0]= 0.00000e+00
  224.       posres-comB[1]= 0.00000e+00
  225.       posres-comB[2]= 0.00000e+00
  226.    QMMM                           = false
  227.    QMconstraints                  = 0
  228.    QMMMscheme                     = 0
  229.    MMChargeScaleFactor            = 1
  230. qm-opts:
  231.    ngQM                           = 0
  232.    constraint-algorithm           = Lincs
  233.    continuation                   = true
  234.    Shake-SOR                      = false
  235.    shake-tol                      = 0.0001
  236.    lincs-order                    = 4
  237.    lincs-iter                     = 1
  238.    lincs-warnangle                = 30
  239.    nwall                          = 0
  240.    wall-type                      = 9-3
  241.    wall-r-linpot                  = -1
  242.    wall-atomtype[0]               = -1
  243.    wall-atomtype[1]               = -1
  244.    wall-density[0]                = 0
  245.    wall-density[1]                = 0
  246.    wall-ewald-zfac                = 3
  247.    pull                           = false
  248.    awh                            = false
  249.    rotation                       = false
  250.    interactiveMD                  = false
  251.    disre                          = No
  252.    disre-weighting                = Conservative
  253.    disre-mixed                    = false
  254.    dr-fc                          = 1000
  255.    dr-tau                         = 0
  256.    nstdisreout                    = 100
  257.    orire-fc                       = 0
  258.    orire-tau                      = 0
  259.    nstorireout                    = 100
  260.    free-energy                    = no
  261.    cos-acceleration               = 0
  262.    deform (3x3):
  263.       deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
  264.       deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
  265.       deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
  266.    simulated-tempering            = false
  267.    swapcoords                     = no
  268.    userint1                       = 0
  269.    userint2                       = 0
  270.    userint3                       = 0
  271.    userint4                       = 0
  272.    userreal1                      = 0
  273.    userreal2                      = 0
  274.    userreal3                      = 0
  275.    userreal4                      = 0
  276.    applied-forces:
  277.      electric-field:
  278.        x:
  279.          E0                       = 0
  280.          omega                    = 0
  281.          t0                       = 0
  282.          sigma                    = 0
  283.        y:
  284.          E0                       = 0
  285.          omega                    = 0
  286.          t0                       = 0
  287.          sigma                    = 0
  288.        z:
  289.          E0                       = 0
  290.          omega                    = 0
  291.          t0                       = 0
  292.          sigma                    = 0
  293. grpopts:
  294.    nrdf:     3895.83     63837.2
  295.    ref-t:         300         300
  296.    tau-t:         0.1         0.1
  297. annealing:          No          No
  298. annealing-npoints:           0           0
  299.    acc:            0           0           0
  300.    nfreeze:           N           N           N
  301.    energygrp-flags[  0]: 0
  302.  
  303. Changing nstlist from 10 to 100, rlist from 1 to 1.167
  304.  
  305. Using 1 MPI thread
  306. Using 16 OpenMP threads
  307.  
  308. 1 GPU auto-selected for this run.
  309. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
  310.   PP:0,PME:0
  311.  
  312. NOTE: GROMACS was configured without NVML support hence it can not exploit
  313.       application clocks of the detected Quadro M2000 GPU to improve performance.
  314.       Recompile with the NVML library (compatible with the driver used) or set application clocks manually.
  315.  
  316. NOTE: GROMACS was configured without NVML support hence it can not exploit
  317.       application clocks of the detected Quadro M2000 GPU to improve performance.
  318.       Recompile with the NVML library (compatible with the driver used) or set application clocks manually.
  319.  
  320. Pinning threads with an auto-selected logical core stride of 1
  321. System total charge: -0.000
  322. Will do PME sum in reciprocal space for electrostatic interactions.
  323.  
  324. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  325. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
  326. A smooth particle mesh Ewald method
  327. J. Chem. Phys. 103 (1995) pp. 8577-8592
  328. -------- -------- --- Thank You --- -------- --------
  329.  
  330. Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
  331. Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
  332. Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
  333.  
  334. Long Range LJ corr.: <C6> 3.1923e-04
  335. Generated table with 1083 data points for Ewald.
  336. Tabscale = 500 points/nm
  337. Generated table with 1083 data points for LJ6.
  338. Tabscale = 500 points/nm
  339. Generated table with 1083 data points for LJ12.
  340. Tabscale = 500 points/nm
  341. Generated table with 1083 data points for 1-4 COUL.
  342. Tabscale = 500 points/nm
  343. Generated table with 1083 data points for 1-4 LJ6.
  344. Tabscale = 500 points/nm
  345. Generated table with 1083 data points for 1-4 LJ12.
  346. Tabscale = 500 points/nm
  347.  
  348. Using GPU 8x8 nonbonded short-range kernels
  349.  
  350. Using a dual 8x4 pair-list setup updated with dynamic, rolling pruning:
  351.   outer list: updated every 100 steps, buffer 0.167 nm, rlist 1.167 nm
  352.   inner list: updated every  10 steps, buffer 0.002 nm, rlist 1.002 nm
  353. At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  354.   outer list: updated every 100 steps, buffer 0.319 nm, rlist 1.319 nm
  355.   inner list: updated every  10 steps, buffer 0.043 nm, rlist 1.043 nm
  356.  
  357. Using geometric Lennard-Jones combination rule
  358.  
  359.  
  360. Initializing LINear Constraint Solver
  361.  
  362. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  363. B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
  364. LINCS: A Linear Constraint Solver for molecular simulations
  365. J. Comp. Chem. 18 (1997) pp. 1463-1472
  366. -------- -------- --- Thank You --- -------- --------
  367.  
  368. The number of constraints is 1984
  369.  
  370. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  371. S. Miyamoto and P. A. Kollman
  372. SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
  373. Water Models
  374. J. Comp. Chem. 13 (1992) pp. 952-962
  375. -------- -------- --- Thank You --- -------- --------
  376.  
  377.  
  378. Intra-simulation communication will occur every 10 steps.
  379. Center of mass motion removal mode is Linear
  380. We have the following groups for center of mass motion removal:
  381.   0:  rest
  382.  
  383. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
  384. G. Bussi, D. Donadio and M. Parrinello
  385. Canonical sampling through velocity rescaling
  386. J. Chem. Phys. 126 (2007) pp. 014101
  387. -------- -------- --- Thank You --- -------- --------
  388.  
  389. There are: 33876 Atoms
  390.  
  391. Started mdrun on rank 0 Wed Feb 28 19:23:24 2018
  392.            Step           Time
  393.               0        0.00000
  394.  
  395.    Energies (kJ/mol)
  396.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  397.     3.93091e+03    2.23591e+02    1.86111e+03    2.95927e+03    7.96031e+03
  398.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  399.     9.30618e+04   -4.56887e+03   -6.35016e+05    2.98154e+03   -5.26606e+05
  400.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  401.     8.55246e+04   -4.41082e+05   -4.41062e+05    3.03729e+02   -2.26420e+02
  402.  Pressure (bar)   Constr. rmsd
  403.    -1.93727e+02    3.02841e-05
  404.  
  405. step  200: timed with pme grid 44 44 44, coulomb cutoff 1.000: 1307.4 M-cycles
  406. step  400: timed with pme grid 40 40 40, coulomb cutoff 1.086: 1100.7 M-cycles
  407. step  600: timed with pme grid 36 36 36, coulomb cutoff 1.206: 1312.0 M-cycles
  408. step  800: timed with pme grid 40 40 40, coulomb cutoff 1.086: 1823.3 M-cycles
  409. step 1000: timed with pme grid 42 42 42, coulomb cutoff 1.034: 1084.8 M-cycles
  410.               optimal pme grid 42 42 42, coulomb cutoff 1.034
  411.            Step           Time
  412.            5000       10.00000
  413.  
  414.    Energies (kJ/mol)
  415.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  416.     3.81408e+03    2.51000e+02    1.81001e+03    2.96705e+03    7.97187e+03
  417.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  418.     9.40692e+04   -4.55248e+03   -6.35642e+05    2.55562e+03   -5.26756e+05
  419.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  420.     8.52103e+04   -4.41546e+05   -4.41190e+05    3.02613e+02   -2.24801e+02
  421.  Pressure (bar)   Constr. rmsd
  422.    -4.12874e+01    2.88478e-05
  423.  
  424.            Step           Time
  425.           10000       20.00000
  426.  
  427.    Energies (kJ/mol)
  428.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  429.     3.74535e+03    2.53348e+02    1.80359e+03    3.01105e+03    7.98561e+03
  430.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  431.     9.51157e+04   -4.58103e+03   -6.37033e+05    2.61371e+03   -5.27086e+05
  432.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  433.     8.38874e+04   -4.43198e+05   -4.41344e+05    2.97915e+02   -2.27625e+02
  434.  Pressure (bar)   Constr. rmsd
  435.     2.01994e+02    2.80778e-05
  436.  
  437.            Step           Time
  438.           15000       30.00000
  439.  
  440.    Energies (kJ/mol)
  441.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  442.     3.79862e+03    2.59292e+02    1.90375e+03    3.03269e+03    7.96951e+03
  443.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  444.     9.41853e+04   -4.57276e+03   -6.35089e+05    2.62000e+03   -5.25892e+05
  445.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  446.     8.49289e+04   -4.40963e+05   -4.41500e+05    3.01614e+02   -2.26806e+02
  447.  Pressure (bar)   Constr. rmsd
  448.     1.95475e+02    2.73920e-05
  449.  
  450.            Step           Time
  451.           20000       40.00000
  452.  
  453.    Energies (kJ/mol)
  454.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  455.     3.74591e+03    2.28070e+02    1.75276e+03    3.00774e+03    7.98380e+03
  456.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  457.     9.40194e+04   -4.55143e+03   -6.35599e+05    2.64141e+03   -5.26771e+05
  458.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  459.     8.43733e+04   -4.42398e+05   -4.41652e+05    2.99641e+02   -2.24697e+02
  460.  Pressure (bar)   Constr. rmsd
  461.    -3.63672e+01    2.73290e-05
  462.  
  463.            Step           Time
  464.           25000       50.00000
  465.  
  466.    Energies (kJ/mol)
  467.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  468.     3.80273e+03    2.54673e+02    1.92893e+03    3.02312e+03    8.02556e+03
  469.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  470.     9.46986e+04   -4.56388e+03   -6.36070e+05    2.63326e+03   -5.26267e+05
  471.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  472.     8.44835e+04   -4.41783e+05   -4.41807e+05    3.00032e+02   -2.25926e+02
  473.  Pressure (bar)   Constr. rmsd
  474.     5.20514e+01    2.84891e-05
  475.  
  476.            Step           Time
  477.           30000       60.00000
  478.  
  479.    Energies (kJ/mol)
  480.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  481.     3.64308e+03    2.69114e+02    1.83624e+03    2.93642e+03    7.83512e+03
  482.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  483.     9.43847e+04   -4.59050e+03   -6.36923e+05    2.60790e+03   -5.28001e+05
  484.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  485.     8.40652e+04   -4.43935e+05   -4.41969e+05    2.98547e+02   -2.28567e+02
  486.  Pressure (bar)   Constr. rmsd
  487.     7.11596e+01    2.80504e-05
  488.  
  489.            Step           Time
  490.           35000       70.00000
  491.  
  492.    Energies (kJ/mol)
  493.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  494.     3.87271e+03    2.44179e+02    1.80161e+03    2.99087e+03    7.94890e+03
  495.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  496.     9.32448e+04   -4.55680e+03   -6.34207e+05    2.60742e+03   -5.26053e+05
  497.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  498.     8.49437e+04   -4.41109e+05   -4.42120e+05    3.01666e+02   -2.25227e+02
  499.  Pressure (bar)   Constr. rmsd
  500.     5.37758e+01    2.68758e-05
  501.  
  502.            Step           Time
  503.           40000       80.00000
  504.  
  505.    Energies (kJ/mol)
  506.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  507.     3.76080e+03    2.54442e+02    1.68395e+03    2.99437e+03    7.98869e+03
  508.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  509.     9.39502e+04   -4.55675e+03   -6.35655e+05    2.65420e+03   -5.26925e+05
  510.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  511.     8.38598e+04   -4.43065e+05   -4.42280e+05    2.97817e+02   -2.25222e+02
  512.  Pressure (bar)   Constr. rmsd
  513.    -2.89238e+01    2.84841e-05
  514.  
  515.            Step           Time
  516.           45000       90.00000
  517.  
  518.    Energies (kJ/mol)
  519.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  520.     3.80936e+03    2.40365e+02    1.84157e+03    3.05451e+03    7.98200e+03
  521.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  522.     9.32492e+04   -4.57017e+03   -6.33466e+05    2.58495e+03   -5.25274e+05
  523.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  524.     8.52468e+04   -4.40027e+05   -4.42441e+05    3.02742e+02   -2.26549e+02
  525.  Pressure (bar)   Constr. rmsd
  526.     1.18503e+02    2.59903e-05
  527.  
  528.            Step           Time
  529.           50000      100.00000
  530.  
  531. Writing checkpoint, step 50000 at Wed Feb 28 19:25:57 2018
  532.  
  533.  
  534.    Energies (kJ/mol)
  535.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  536.     4.05700e+03    2.79840e+02    1.79805e+03    2.97583e+03    7.94072e+03
  537.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  538.     9.30207e+04   -4.57038e+03   -6.33621e+05    2.60657e+03   -5.25513e+05
  539.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  540.     8.53900e+04   -4.40123e+05   -4.42616e+05    3.03251e+02   -2.26570e+02
  541.  Pressure (bar)   Constr. rmsd
  542.    -2.43613e+01    2.94082e-05
  543.  
  544.     <======  ###############  ==>
  545.     <====  A V E R A G E S  ====>
  546.     <==  ###############  ======>
  547.  
  548.     Statistics over 50001 steps using 501 frames
  549.  
  550.    Energies (kJ/mol)
  551.           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
  552.     3.82827e+03    2.51703e+02    1.81002e+03    2.98604e+03    7.96516e+03
  553.         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
  554.     9.37059e+04   -4.56099e+03   -6.34690e+05    2.60131e+03   -5.26103e+05
  555.     Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
  556.     8.44456e+04   -4.41657e+05   -4.41814e+05    2.99897e+02   -2.25642e+02
  557.  Pressure (bar)   Constr. rmsd
  558.     7.31157e+00    0.00000e+00
  559.  
  560.           Box-X          Box-Y          Box-Z
  561.     6.95241e+00    6.95241e+00    6.95241e+00
  562.  
  563.    Total Virial (kJ/mol)
  564.     2.81735e+04    2.20717e+01    5.10171e+00
  565.     2.23885e+01    2.80795e+04    5.39179e+01
  566.     4.22678e+00    5.37247e+01    2.79740e+04
  567.  
  568.    Pressure (bar)
  569.    -5.58816e-01   -2.01430e+00   -4.64558e-01
  570.    -2.04569e+00    5.29394e+00   -5.85250e+00
  571.    -3.78313e-01   -5.83325e+00    1.71996e+01
  572.  
  573.       T-Protein  T-non-Protein
  574.     2.99902e+02    2.99897e+02
  575.  
  576.  
  577.        P P   -   P M E   L O A D   B A L A N C I N G
  578.  
  579.  PP/PME load balancing changed the cut-off and PME settings:
  580.            particle-particle                    PME
  581.             rcoulomb  rlist            grid      spacing   1/beta
  582.    initial  1.000 nm  1.002 nm      44  44  44   0.158 nm  0.320 nm
  583.    final    1.034 nm  1.036 nm      42  42  42   0.165 nm  0.331 nm
  584.  cost-ratio           1.11             0.87
  585.  (note that these numbers concern only part of the total PP and PME load)
  586.  
  587.  
  588.     M E G A - F L O P S   A C C O U N T I N G
  589.  
  590.  NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
  591.  RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
  592.  W3=SPC/TIP3p  W4=TIP4p (single or pairs)
  593.  V&F=Potential and force  V=Potential only  F=Force only
  594.  
  595.  Computing:                               M-Number         M-Flops  % Flops
  596. -----------------------------------------------------------------------------
  597.  Pair Search distance check            1686.672592       15180.053     0.0
  598.  NxN Ewald Elec. + LJ [F]           1745297.579520   115189640.248    98.1
  599.  NxN Ewald Elec. + LJ [V&F]           17664.491264     1890100.565     1.6
  600.  1,4 nonbonded interactions             255.305106       22977.460     0.0
  601.  Shift-X                                 16.971876         101.831     0.0
  602.  Angles                                 177.353547       29795.396     0.0
  603.  Propers                                 21.300426        4877.798     0.0
  604.  RB-Dihedrals                           197.503950       48783.476     0.0
  605.  Virial                                 169.638921        3053.501     0.0
  606.  Stop-CM                                 16.971876         169.719     0.0
  607.  Calc-Ekin                              338.827752        9148.349     0.0
  608.  Lincs                                   99.201984        5952.119     0.0
  609.  Lincs-Mat                             2128.242564        8512.970     0.0
  610.  Constraint-V                          1793.835876       14350.687     0.0
  611.  Constraint-Vir                         169.493892        4067.853     0.0
  612.  Settle                                 531.810636      171774.835     0.1
  613. -----------------------------------------------------------------------------
  614.  Total                                               117418486.861   100.0
  615. -----------------------------------------------------------------------------
  616.  
  617.  
  618.      R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
  619.  
  620. On 1 MPI rank, each using 16 OpenMP threads
  621.  
  622.  Computing:          Num   Num      Call    Wall time         Giga-Cycles
  623.                      Ranks Threads  Count      (s)         total sum    %
  624. -----------------------------------------------------------------------------
  625.  Neighbor search        1   16        501       0.985         59.244   0.6
  626.  Launch GPU ops.        1   16     100002       4.723        284.115   3.1
  627.  Force                  1   16      50001       4.152        249.763   2.7
  628.  Wait PME GPU gather    1   16      50001      25.177       1514.681  16.4
  629.  Reduce GPU PME F       1   16      50001       7.821        470.510   5.1
  630.  Wait GPU NB local      1   16      50001      83.009       4993.925  54.2
  631.  NB X/F buffer ops.     1   16      99501       9.648        580.431   6.3
  632.  Write traj.            1   16         11       0.202         12.158   0.1
  633.  Update                 1   16      50001       3.917        235.623   2.6
  634.  Constraints            1   16      50001       7.526        452.791   4.9
  635.  Rest                                           5.976        359.543   3.9
  636. -----------------------------------------------------------------------------
  637.  Total                                        153.135       9212.785 100.0
  638. -----------------------------------------------------------------------------
  639.  
  640.                Core t (s)   Wall t (s)        (%)
  641.        Time:     2450.154      153.135     1600.0
  642.                  (ns/day)    (hour/ns)
  643. Performance:       56.422        0.425
  644. Finished mdrun on rank 0 Wed Feb 28 19:25:57 2018
RAW Paste Data
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy. OK, I Understand
 
Top