:-) GROMACS - gmx mdrun, 2023.1 (-: Copyright 1991-2023 The GROMACS Authors. 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. Current GROMACS contributors: Mark Abraham Andrey Alekseenko Cathrine Bergh Christian Blau Eliane Briand Mahesh Doijade Stefan Fleischmann Vytas Gapsys Gaurav Garg Sergey Gorelov Gilles Gouaillardet Alan Gray M. Eric Irrgang Farzaneh Jalalypour Joe Jordan Christoph Junghans Prashanth Kanduri Sebastian Keller Carsten Kutzner Justin A. Lemkul Magnus Lundborg Pascal Merz Vedran Miletic Dmitry Morozov Szilard Pall Roland Schulz Michael Shirts Alexey Shvetsov Balint Soproni David van der Spoel Philip Turner Carsten Uphoff Alessandra Villa Sebastian Wingbermuehle Artem Zhmurov Previous GROMACS contributors: Emile Apol Rossen Apostolov James Barnett Herman J.C. Berendsen Par Bjelkmar Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Carlo Camilloni Rudi van Drunen Anton Feenstra Oliver Fleetwood Gerrit Groenhof Bert de Groot Anca Hamuraru Vincent Hindriksen Victor Holanda Aleksei Iupinov Dimitrios Karkoulis Peter Kasson Sebastian Kehl Jiri Kraus Per Larsson Viveca Lindahl Erik Marklund Pieter Meulenhoff Teemu Murtola Sander Pronk Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Coordinated by the GROMACS project leaders: Paul Bauer, Berk Hess, and Erik Lindahl GROMACS: gmx mdrun, version 2023.1 Executable: /amorphous/apps/gromacs-2023.1/bin/gmx Data prefix: /amorphous/apps/gromacs-2023.1 Working dir: ************************************************** Process ID: 13640 Command line: gmx mdrun -v -deffnm step6.1_equilibration -ntmpi 8 -npme 1 -pme gpu -update cpu -nb gpu -bonded gpu GROMACS version: 2023.1 Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) GPU support: CUDA NB cluster size: 8 SIMD instructions: AVX2_256 CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128 GPU FFT library: cuFFT Multi-GPU FFT: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /amorphous/apps/gcc-10.3.0/bin/gcc GNU 10.3.0 C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG C++ compiler: /amorphous/apps/gcc-10.3.0/bin/g++ GNU 10.3.0 C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG BLAS library: External - detected on the system LAPACK library: External - detected on the system CUDA compiler: /amorphous/apps/cuda/11.8-gcc-10.3.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2022 NVIDIA Corporation;Built on Wed_Sep_21_10:33:58_PDT_2022;Cuda compilation tools, release 11.8, V11.8.89;Build cuda_11.8.r11.8/compiler.31833905_0 CUDA compiler flags:-std=c++17;--generate-code=arch=compute_35,code=sm_35;--generate-code=arch=compute_37,code=sm_37;--generate-code=arch=compute_50,code=sm_50;--generate-code=arch=compute_52,code=sm_52;--generate-code=arch=compute_60,code=sm_60;--generate-code=arch=compute_61,code=sm_61;--generate-code=arch=compute_70,code=sm_70;--generate-code=arch=compute_75,code=sm_75;--generate-code=arch=compute_80,code=sm_80;--generate-code=arch=compute_86,code=sm_86;--generate-code=arch=compute_89,code=sm_89;--generate-code=arch=compute_90,code=sm_90;-Wno-deprecated-gpu-targets;--generate-code=arch=compute_53,code=sm_53;--generate-code=arch=compute_80,code=sm_80;-use_fast_math;-Xptxas;-warn-double-usage;-Xptxas;-Werror;;-fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG CUDA driver: 12.0 CUDA runtime: 11.80 Running on 1 node with total 32 cores, 32 processing units, 4 compatible GPUs Hardware detected on host gx03: CPU info: Vendor: AMD Brand: AMD EPYC 7502P 32-Core Processor Family: 23 Model: 49 Stepping: 0 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 Hardware topology: Basic Packages, cores, and logical processors: [indices refer to OS logical processors] Package 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] [ 14] [ 15] [ 16] [ 17] [ 18] [ 19] [ 20] [ 21] [ 22] [ 23] [ 24] [ 25] [ 26] [ 27] [ 28] [ 29] [ 30] [ 31] CPU limit set by OS: -1 Recommended max number of threads: 32 GPU info: Number of GPUs detected: 4 #0: NVIDIA NVIDIA GeForce RTX 3090, compute cap.: 8.6, ECC: no, stat: compatible #1: NVIDIA NVIDIA GeForce RTX 3090, compute cap.: 8.6, ECC: no, stat: compatible #2: NVIDIA NVIDIA GeForce RTX 3090, compute cap.: 8.6, ECC: no, stat: compatible #3: NVIDIA NVIDIA GeForce RTX 3090, compute cap.: 8.6, 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 --- -------- -------- ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++ https://doi.org/10.5281/zenodo.7852175 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.001 nsteps = 20000 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -14716115 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 1000 nstfout = 1000 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 1000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 20 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 = Force-switch rvdw-switch = 1 rvdw = 1.2 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier-nx = 112 fourier-ny = 112 fourier-nz = 128 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 3d epsilon-surface = 0 ensemble-temperature-setting = auto ensemble-temperature = -1 tcoupl = V-rescale nsttcouple = 100 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p (3x3): ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+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 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 density-guided-simulation: active = false group = protein similarity-measure = inner-product atom-spreading-weight = unity force-constant = 1e+09 gaussian-transform-spreading-width = 0.2 gaussian-transform-spreading-range-in-multiples-of-width = 4 reference-density-filename = reference.mrc nst = 1 normalize-densities = true adaptive-force-scaling = false adaptive-force-scaling-time-constant = 4 shift-vector = transformation-matrix = qmmm-cp2k: active = false qmgroup = System qmmethod = PBE qmfilenames = qmcharge = 0 qmmultiplicity = 1 grpopts: nrdf: 21845.6 147197 327888 ref-t: 1 1 1 tau-t: 1 1 1 annealing: Single Single Single annealing-npoints: 2 2 2 annealing-time [0]: 0.0 20.0 annealing-temp [0]: 1.0 100.0 annealing-time [1]: 0.0 20.0 annealing-temp [1]: 1.0 100.0 annealing-time [2]: 0.0 20.0 annealing-temp [2]: 1.0 100.0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 Update groups can not be used for this system because atoms that are (in)directly constrained together are interdispersed with other atoms Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.021 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.524 nm, LJ-14, atoms 56 62 multi-body bonded interactions: 0.524 nm, Proper Dih., atoms 56 62 Minimum cell size due to bonded interactions: 0.576 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm Estimated maximum distance required for P-LINCS: 0.222 nm Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Using 1 separate PME ranks, as requested with -npme option Optimizing the DD grid for 7 cells with a minimum initial size of 0.720 nm The maximum allowed number of cells is: X 18 Y 18 Z 20 Domain decomposition grid 1 x 1 x 7, separate PME ranks 1 PME domain decomposition: 1 x 1 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: Z 1 The initial domain decomposition cell size is: Z 2.11 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 1.200 nm multi-body bonded interactions (-rdd) 1.200 nm atoms separated by up to 5 constraints (-rcon) 2.110 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: Z 1 The minimum size for domain decomposition cells is 1.200 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: Z 0.57 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 1.200 nm multi-body bonded interactions (-rdd) 1.200 nm atoms separated by up to 5 constraints (-rcon) 1.200 nm On host gx03 4 GPUs selected for this run. Mapping of GPU IDs to the 8 GPU tasks in the 8 ranks on this node: PP:0,PP:0,PP:1,PP:1,PP:2,PP:2,PP:3,PME:3 PP tasks will do (non-perturbed) short-ranged and most bonded interactions on the GPU PP task will update and constrain coordinates on the CPU PME tasks will do all aspects on the GPU Using 8 MPI threads Using 4 OpenMP threads per tMPI thread 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: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06 Initialized non-bonded Coulomb Ewald tables, spacing: 1.02e-03 size: 1176 Generated table with 1100 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ12. Tabscale = 500 points/nm Using GPU 8x8 nonbonded short-range kernels Using a 8x8 pair-list setup: updated every 100 steps, buffer 0.000 nm, rlist 1.200 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: updated every 100 steps, buffer 0.000 nm, rlist 1.200 nm Removing pbc first time Linking all bonded interactions to atoms Pinning threads with an auto-selected logical cpu stride of 1 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 42145 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 --- -------- -------- Intra-simulation communication will occur every 100 steps. ++++ 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: 234189 Atoms Atom distribution over 7 domains: av 33455 stddev 1694 min 30602 max 34797 NOTE: DLB will not turn on during the first phase of PME tuning Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: SOLU_MEMB 1: SOLV RMS relative constraint deviation after constraining: 2.26e-06 Initial temperature: 1.00088 K Started mdrun on rank 0 Wed May 31 20:34:52 2023 Step Time 0 0.00000