Log file opened on Wed Jun 20 00:21:32 2018 Host: vlad pid: 2520 rank ID: 0 number of ranks: 1 :-) GROMACS - gmx mdrun, 2018 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2018 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/vlad/study/epidermin/ep_run/run_dp/extra Command line: gmx mdrun -s md.tpr -deffnm MD GROMACS version: 2018 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: CUDA SIMD instructions: AVX_512 FFT library: fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled Built on: 2018-06-13 00:12:23 Built by: vlad@vlad [CMAKE] Build OS/arch: Linux 4.13.0-45-generic x86_64 Build CPU vendor: Intel Build CPU brand: Intel(R) Core(TM) i7-7820X CPU @ 3.60GHz Build CPU family: 6 Model: 85 Stepping: 4 Build CPU features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 5.4.0 C compiler flags: -mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 5.4.0 C++ compiler flags: -mavx512f -mfma -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on Wed_Apr_11_23:16:29_CDT_2018;Cuda compilation tools, release 9.2, V9.2.88 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;; ;-mavx512f;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; CUDA driver: 9.20 CUDA runtime: 9.20 Running on 1 node with total 8 cores, 16 logical cores, 1 compatible GPU Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Core(TM) i7-7820X CPU @ 3.60GHz Family: 6 Model: 85 Stepping: 4 Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Number of AVX-512 FMA units: 2 Hardware topology: Basic Sockets, cores, and logical processors: Socket 0: [ 0 8] [ 1 9] [ 2 10] [ 3 11] [ 4 12] [ 5 13] [ 6 14] [ 7 15] GPU info: Number of GPUs detected: 1 #0: NVIDIA TITAN Xp, compute cap.: 6.1, ECC: no, stat: compatible ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers SoftwareX 1 (2015) pp. 19-25 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 (2013) pp. 845-54 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 25000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 10 bd-fric = 0 ld-seed = 1266334194 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 50000 nstvout = 500000 nstfout = 0 nstlog = 10000 nstcalcenergy = 10 nstenergy = 10000 nstxout-compressed = 5000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 ns-type = Grid pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.2 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 1.2 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 fourier-nx = 80 fourier-ny = 80 fourier-nz = 80 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 implicit-solvent = No gb-algorithm = Still nstgbradii = 1 rgbradii = 1 gb-epsilon-solvent = 80 gb-saltconc = 0 gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation sa-surface-tension = 2.05016 tcoupl = V-rescale nsttcouple = 10 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = Berendsen pcoupltype = Isotropic nstpcouple = 10 tau-p = 1 compressibility (3x3): compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} ref-p (3x3): ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = false QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = false Shake-SOR = false shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = false awh = false rotation = false interactiveMD = false disre = No disre-weighting = Conservative disre-mixed = false dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} simulated-tempering = false swapcoords = no userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 applied-forces: electric-field: x: E0 = 0 omega = 0 t0 = 0 sigma = 0 y: E0 = 0 omega = 0 t0 = 0 sigma = 0 z: E0 = 0 omega = 0 t0 = 0 sigma = 0 grpopts: nrdf: 64035 277.975 ref-t: 315 315 tau-t: 0.1 0.1 annealing: No No annealing-npoints: 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Changing nstlist from 10 to 100, rlist from 1.2 to 1.214 Using 1 MPI thread Using 8 OpenMP threads 1 GPU auto-selected for this run. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node: PP:0,PME:0 Pinning threads with an auto-selected logical core stride of 2 System total charge: 0.000 Will do PME sum in reciprocal space for electrostatic interactions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -8.333e-06 Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176 Long Range LJ corr.: 7.3672e-03 Generated table with 1107 data points for Ewald. Tabscale = 500 points/nm Generated table with 1107 data points for LJ6. Tabscale = 500 points/nm Generated table with 1107 data points for LJ12. Tabscale = 500 points/nm Generated table with 1107 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1107 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1107 data points for 1-4 LJ12. Tabscale = 500 points/nm Using GPU 8x8 nonbonded short-range kernels Using a 8x4 pair-list setup: updated every 100 steps, buffer 0.014 nm, rlist 1.214 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: updated every 100 steps, buffer 0.121 nm, rlist 1.321 nm Using full Lennard-Jones parameter combination matrix Removing pbc first time Initializing LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 -------- -------- --- Thank You --- -------- -------- The number of constraints is 21478 Intra-simulation communication will occur every 10 steps. Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: Protein 1: non-Protein ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 -------- -------- --- Thank You --- -------- -------- There are: 28599 Atoms Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 2.52e-06 Initial temperature: 314.916 K Started mdrun on rank 0 Wed Jun 20 00:21:34 2018 Step Time 0 0.00000 Energies (kJ/mol) Angle G96Angle Proper Dih. Improper Dih. LJ-14 2.67456e+04 1.01453e+03 2.11457e+02 2.63045e+03 1.41570e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -7.06860e+03 -2.16011e+05 -1.79004e+04 -1.51898e+05 6.05049e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -3.56084e+05 8.42057e+04 -2.71879e+05 -2.71881e+05 3.14948e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -3.65709e+02 8.26737e+01 6.04419e-05 step 200: timed with pme grid 80 80 80, coulomb cutoff 1.200: 252.6 M-cycles step 400: timed with pme grid 64 64 64, coulomb cutoff 1.459: 265.1 M-cycles step 600: timed with pme grid 56 56 56, coulomb cutoff 1.668: 282.9 M-cycles step 800: timed with pme grid 48 48 48, coulomb cutoff 1.946: 344.2 M-cycles step 1000: timed with pme grid 52 52 52, coulomb cutoff 1.796: 303.8 M-cycles step 1200: timed with pme grid 56 56 56, coulomb cutoff 1.668: 256.0 M-cycles step 1400: timed with pme grid 60 60 60, coulomb cutoff 1.556: 240.5 M-cycles step 1600: timed with pme grid 64 64 64, coulomb cutoff 1.459: 228.7 M-cycles step 1800: timed with pme grid 72 72 72, coulomb cutoff 1.297: 217.1 M-cycles step 2000: timed with pme grid 80 80 80, coulomb cutoff 1.200: 211.2 M-cycles step 2200: timed with pme grid 64 64 64, coulomb cutoff 1.459: 229.6 M-cycles step 2400: timed with pme grid 72 72 72, coulomb cutoff 1.297: 218.8 M-cycles step 2600: timed with pme grid 80 80 80, coulomb cutoff 1.200: 214.2 M-cycles optimal pme grid 80 80 80, coulomb cutoff 1.200 Step Time 10000 20.00000 Energies (kJ/mol) Angle G96Angle Proper Dih. Improper Dih. LJ-14 2.65583e+04 9.43022e+02 2.32472e+02 2.63906e+03 1.66363e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -6.94323e+03 -2.15861e+05 -1.78981e+04 -1.52406e+05 5.90547e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -3.56664e+05 8.37825e+04 -2.72881e+05 -2.72235e+05 3.13365e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -3.65613e+02 7.00818e+01 6.52835e-05 Step Time 20000 40.00000 Energies (kJ/mol) Angle G96Angle Proper Dih. Improper Dih. LJ-14 2.65154e+04 1.03761e+03 2.17551e+02 2.57333e+03 1.44425e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -7.07706e+03 -2.16273e+05 -1.79033e+04 -1.51812e+05 5.93652e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -3.56640e+05 8.28835e+04 -2.73757e+05 -2.73205e+05 3.10003e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -3.65828e+02 2.00369e+01 6.60739e-05 Step Time 25000 50.00000 Writing checkpoint, step 25000 at Wed Jun 20 00:21:53 2018 Energies (kJ/mol) Angle G96Angle Proper Dih. Improper Dih. LJ-14 2.63248e+04 9.31751e+02 1.88464e+02 2.61446e+03 1.63635e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -6.87959e+03 -2.16322e+05 -1.79132e+04 -1.52130e+05 5.98868e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -3.57034e+05 8.44403e+04 -2.72593e+05 -2.73247e+05 3.15825e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -3.66230e+02 2.45971e+01 6.85766e-05 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 25001 steps using 2501 frames Energies (kJ/mol) Angle G96Angle Proper Dih. Improper Dih. LJ-14 2.64645e+04 9.60188e+02 1.99680e+02 2.61917e+03 1.51584e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -6.95103e+03 -2.16403e+05 -1.79086e+04 -1.51770e+05 5.68046e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -3.56957e+05 8.42448e+04 -2.72712e+05 -2.72648e+05 3.15094e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -3.66043e+02 6.93445e-01 0.00000e+00 Box-X Box-Y Box-Z 9.33708e+00 9.33708e+00 9.33708e+00 Total Virial (kJ/mol) 2.80517e+04 -5.46261e+01 8.44450e+01 -5.46254e+01 2.81100e+04 -1.37755e+02 8.44485e+01 -1.37757e+02 2.80322e+04 Pressure (bar) 1.55005e+00 3.21133e+00 -4.00804e+00 3.21130e+00 -1.87748e+00 5.46438e+00 -4.00818e+00 5.46445e+00 2.40777e+00 T-SOL T-not_SOL 3.15088e+02 3.16400e+02 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- Pair Search distance check 363.109440 3267.985 0.0 NxN Ewald Elec. + LJ [F] 358907.564160 23687899.235 84.1 NxN Ewald Elec. + LJ [V&F] 39893.740608 4268630.245 15.2 1,4 nonbonded interactions 5.650226 508.520 0.0 Shift-X 7.178349 43.070 0.0 Angles 538.646545 90492.620 0.3 Propers 2.200088 503.820 0.0 Impropers 178.957158 37223.089 0.1 Virial 71.638644 1289.496 0.0 Stop-CM 71.554698 715.547 0.0 P-Coupling 71.526099 429.157 0.0 Calc-Ekin 143.052198 3862.409 0.0 Lincs 537.014434 32220.866 0.1 Lincs-Mat 6464.875692 25859.503 0.1 Constraint-V 1073.985912 8591.887 0.0 Constraint-Vir 53.716478 1289.195 0.0 ----------------------------------------------------------------------------- Total 28162826.644 100.0 ----------------------------------------------------------------------------- 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 On 1 MPI rank, each using 8 OpenMP threads Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Neighbor search 1 8 251 0.312 8.976 1.7 Launch GPU ops. 1 8 50002 1.701 48.997 9.1 Force 1 8 25001 3.960 114.079 21.3 Wait PME GPU gather 1 8 25001 1.592 45.870 8.6 Reduce GPU PME F 1 8 25001 0.113 3.266 0.6 Wait GPU NB local 1 8 25001 2.497 71.918 13.4 NB X/F buffer ops. 1 8 49751 0.941 27.102 5.1 Write traj. 1 8 6 0.079 2.275 0.4 Update 1 8 25001 0.531 15.285 2.9 Constraints 1 8 25001 3.124 89.978 16.8 Rest 3.744 107.848 20.1 ----------------------------------------------------------------------------- Total 18.593 535.594 100.0 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 148.741 18.593 800.0 (ns/day) (hour/ns) Performance: 232.360 0.103 Finished mdrun on rank 0 Wed Jun 20 00:21:53 2018