:-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent 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) 2001-2018, 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 2019.1 Executable: /apps/broadwell/centos7/GROMACS/2019.1-intel-2018b-UArecipe/bin/gmx_mpi Data prefix: /apps/broadwell/centos7/GROMACS/2019.1-intel-2018b-UArecipe Working dir: /scratch/gromacs-2019/2018u3-2019.2 Process ID: 7244 Command line: gmx_mpi mdrun -ntomp 1 -s 0519.tpr -o /scratch/gromacs-2019/2018u3-2019.2/0519.trr -x /scratch/gromacs-2019/2018u3-2019.2/0519.xtc -cpo /scratch/gromacs-2019/2018u3-2019.2/0519.cpt -c /scratch/gromacs-2019/2018u3-2019.2/0519.gro -e /scratch/gromacs-2019/2018u3-2019.2/0519.edr -dhdl /scratch/gromacs-2019/2018u3-2019.2/0519.xvg -g /scratch/gromacs-2019/2018u3-2019.2/0519.log -px /scratch/gromacs-2019/2018u3-2019.2/0519.x.xvg -pf /scratch/gromacs-2019/2018u3-2019.2/0519.f.xvg -noconfout -rcon 0.7 -pin on -dds 0.9 -dlb auto -maxh 1 GROMACS version: 2019.1 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX2_256 FFT library: Intel MKL RDTSCP usage: enabled TNG support: enabled Hwloc support: hwloc-1.11.8 Tracing support: disabled C compiler: /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicc Intel 18.0.3.20180410 C compiler flags: -march=core-avx2 -mkl=sequential -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits C++ compiler: /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicpc Intel 18.0.3.20180410 C++ compiler flags: -march=core-avx2 -mkl=sequential -std=c++11 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits Running on 4 nodes with total 112 cores, 112 logical cores Cores per node: 28 Logical cores per node: 28 Hardware detected on host r3c07cn2 (the node of MPI rank 0): CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Family: 6 Model: 79 Stepping: 1 Features: aes apic avx avx2 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 Hardware topology: Full, with devices Sockets, cores, and logical processors: Socket 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] Socket 1: [ 14] [ 15] [ 16] [ 17] [ 18] [ 19] [ 20] [ 21] [ 22] [ 23] [ 24] [ 25] [ 26] [ 27] Numa nodes: Node 0 (68600541184 bytes mem): 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Node 1 (68719476736 bytes mem): 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Latency: 0 1 0 1.00 2.10 1 2.10 1.00 Caches: L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways L3: 36700160 bytes, linesize 64 bytes, assoc. 20, shared 14 ways PCI devices: 0000:01:00.0 Id: 8086:1521 Class: 0x0200 Numa: 0 0000:01:00.1 Id: 8086:1521 Class: 0x0200 Numa: 0 0000:02:00.0 Id: 15b3:1013 Class: 0x0207 Numa: 0 0000:00:11.4 Id: 8086:8d62 Class: 0x0106 Numa: 0 0000:07:00.0 Id: 1a03:2000 Class: 0x0300 Numa: 0 0000:00:1f.2 Id: 8086:8d02 Class: 0x0106 Numa: 0 ++++ 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 --- -------- -------- ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++ https://doi.org/10.5281/zenodo.2564764 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 500000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -1437393019 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 50000 nstcalcenergy = 100 nstenergy = 50000 nstxout-compressed = 50000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 20 ns-type = Grid pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.223 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 = 1 rvdw = 1.2 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.16 fourier-nx = 96 fourier-ny = 84 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 tcoupl = V-rescale nsttcouple = 20 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = Berendsen pcoupltype = Isotropic nstpcouple = 20 tau-p = 2 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 = COM 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 = true 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 = true pull-cylinder-r = 1.5 pull-constr-tol = 1e-06 pull-print-COM = true pull-print-ref-value = true pull-print-components = true pull-nstxout = 50000 pull-nstfout = 50000 pull-pbc-ref-prev-step-com = false pull-xout-average = false pull-fout-average = false pull-ngroups = 3 pull-group 0: atom: not available weight: not available pbcatom = -1 pull-group 1: atom (1): atom[0]=1442 weight: not available pbcatom = -1 pull-group 2: atom (2): atom[0]=4641 atom[1]=4643 weight: not available pbcatom = 4641 pull-ncoords = 1 pull-coord 0: type = umbrella geometry = distance group[0] = 1 group[1] = 2 dim (3): dim[0]=1 dim[1]=1 dim[2]=1 origin (3): origin[0]= 0.00000e+00 origin[1]= 0.00000e+00 origin[2]= 0.00000e+00 vec (3): vec[0]= 0.00000e+00 vec[1]= 0.00000e+00 vec[2]= 0.00000e+00 start = true init = 0.518654 rate = 0 k = 1000 kB = 1000 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: 12909.9 439152 ref-t: 300 300 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 20 to 80, rlist from 1.223 to 1.326 Initializing Domain Decomposition on 112 ranks Dynamic load balancing: locked Minimum cell size due to atom displacement: 0.514 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.443 nm, LJ-14, atoms 1990 2780 multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1990 2780 Minimum cell size due to bonded interactions: 0.487 nm User supplied maximum distance required for P-LINCS: 0.700 nm Guess for relative PME load: 0.13 Will use 96 particle-particle and 16 PME only ranks This is a guess, check the performance at the end of the log file Using 16 separate PME ranks, as guessed by mdrun Scaling the initial minimum size with 1/0.9 (option -dds) = 1.11111 Optimizing the DD grid for 96 cells with a minimum initial size of 0.778 nm The maximum allowed number of cells is: X 18 Y 17 Z 15 Domain decomposition grid 4 x 4 x 6, separate PME ranks 16 PME domain decomposition: 4 x 4 x 1 Interleaving PP and PME ranks This rank does only particle-particle work. Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 1 Y 1 Z 1 The initial domain decomposition cell size is: X 3.63 nm Y 3.31 nm Z 2.00 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.326 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.326 nm multi-body bonded interactions (-rdd) 1.326 nm atoms separated by up to 5 constraints (-rcon) 2.003 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 Z 1 The minimum size for domain decomposition cells is 1.326 nm The requested allowed shrink of DD cells (option -dds) is: 0.90 The allowed shrink of domain decomposition cells is: X 0.37 Y 0.40 Z 0.66 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.326 nm two-body bonded interactions (-rdd) 1.326 nm multi-body bonded interactions (-rdd) 1.326 nm atoms separated by up to 5 constraints (-rcon) 1.326 nm Using two step summing over 4 groups of on average 24.0 ranks Using 112 MPI processes Using 1 OpenMP thread per MPI process Overriding thread affinity set outside gmx mdrun Pinning threads with an auto-selected logical core stride of 1 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.: 3.1361e-04 Generated table with 1163 data points for Ewald. Tabscale = 500 points/nm Generated table with 1163 data points for LJ6. Tabscale = 500 points/nm Generated table with 1163 data points for LJ12. Tabscale = 500 points/nm Generated table with 1163 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1163 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1163 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SIMD 4x8 nonbonded short-range kernels Using a dual 4x8 pair-list setup updated with dynamic pruning: outer list: updated every 80 steps, buffer 0.126 nm, rlist 1.326 nm inner list: updated every 13 steps, buffer 0.002 nm, rlist 1.202 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 80 steps, buffer 0.275 nm, rlist 1.475 nm inner list: updated every 13 steps, buffer 0.052 nm, rlist 1.252 nm Using full Lennard-Jones parameter combination matrix Will apply potential COM pulling with 1 pull coordinate and 2 groups Pull group 1: 1 atoms, mass 13.019 Pull group 2: 2 atoms, mass 26.018 Will use a sub-communicator for pull communication Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 1073 There are constraints between atoms in different decomposition domains, will communicate selected coordinates each lincs iteration ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- Linking all bonded interactions to atoms The -noconfout functionality is deprecated, and may be removed in a future version. Intra-simulation communication will occur every 20 steps. Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest ++++ 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: 224238 Atoms Atom distribution over 96 domains: av 2335 stddev 86 min 2090 max 2430 Started mdrun on rank 0 Mon Apr 29 22:52:24 2019 Step Time 0 0.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 5.09960e+03 7.77425e+03 4.85656e+03 2.47900e+03 -1.61705e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.64263e+04 5.11422e+05 -1.65591e+04 -3.68724e+06 1.05264e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 6.82855e-14 -3.09538e+06 9.65238e+03 -3.08573e+06 -3.08550e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 5.13609e+00 -1.19286e+02 -1.38954e+03 2.44671e-06