:-) GROMACS - gmx mdrun, 2022.1 (-: Copyright 1991-2022 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 Kevin Boyd Oliver Fleetwood Stefan Fleischmann Vytas Gapsys Gaurav Garg Gilles Gouaillardet Alan Gray Victor Holanda M. Eric Irrgang Joe Jordan Christoph Junghans Prashanth Kanduri Sebastian Kehl Sebastian Keller Carsten Kutzner Magnus Lundborg Pascal Merz Dmitry Morozov Szilard Pall Roland Schulz Michael Shirts David van der Spoel Alessandra Villa Sebastian Wingbermuehle Artem Zhmurov Previous GROMACS contributors: Emile Apol Rossen Apostolov James Barnett Herman J.C. Berendsen Par Bjelkmar Viacheslav Bolnykh Aldert van Buuren Carlo Camilloni Rudi van Drunen Anton Feenstra Gerrit Groenhof Bert de Groot Anca Hamuraru Vincent Hindriksen Aleksei Iupinov Dimitrios Karkoulis Peter Kasson Jiri Kraus Per Larsson Justin A. Lemkul Viveca Lindahl Erik Marklund Pieter Meulenhoff Vedran Miletic Teemu Murtola Sander Pronk Alexey Shvetsov 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 2022.1 Executable: /home/j20210168/gromacs-2022/installGIMPI/bin/gmx_GIMPI Data prefix: /home/j20210168/gromacs-2022/installGIMPI Working dir: /scratch/j20210168/PRAGIN/GROMACS/DNA-IL-WATER/NEW_TRIAL/STEP6_NPT_PROD Process ID: 33078 Command line: gmx_GIMPI mdrun -deffnm npt_prod -nb gpu -pme gpu -npme 1 -bonded cpu -update gpu GROMACS version: 2022.1 Precision: mixed Memory model: 64 bit MPI library: MPI (CUDA-aware) OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) GPU support: CUDA SIMD instructions: AVX_512 CPU FFT library: fftw-3.3.8-avx512 GPU FFT library: cuFFT RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /home/j20210168/openmpi-4.1.0/installdir/bin/mpicc GNU 8.3.0 C compiler flags: -mavx512f -mfma -mavx512vl -mavx512dq -mavx512bw -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG C++ compiler: /home/j20210168/openmpi-4.1.0/installdir/bin/mpicxx GNU 8.3.0 C++ compiler flags: -mavx512f -mfma -mavx512vl -mavx512dq -mavx512bw -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG CUDA compiler: /opt/ohpc/pub/cuda-11.2/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2020 NVIDIA Corporation;Built on Mon_Nov_30_19:08:53_PST_2020;Cuda compilation tools, release 11.2, V11.2.67;Build cuda_11.2.r11.2/compiler.29373293_0 CUDA compiler flags:-std=c++17;;;-mavx512f -mfma -mavx512vl -mavx512dq -mavx512bw -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG CUDA driver: 11.70 CUDA runtime: 11.20 Running on 2 nodes with total 4 cores, 4 processing units, 4 compatible GPUs Cores per node: 2 Logical processing units per node: -2 - 2 OS CPU Limit / recommended threads to start per node: 2 Compatible GPUs per node: 2 All nodes have identical type(s) of GPUs Hardware detected on host gpu010.iitkgp.ac.in (the node of MPI rank 0): CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz Family: 6 Model: 85 Stepping: 4 Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA 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 Packages, cores, and logical processors: [indices refer to OS logical processors] Package 0: [ 0] [ 1] CPU limit set by OS: -1 Recommended max number of threads: 2 GPU info: Number of GPUs detected: 2 #0: NVIDIA Tesla V100-PCIE-16GB, compute cap.: 7.0, ECC: yes, stat: compatible #1: NVIDIA Tesla V100-PCIE-16GB, compute cap.: 7.0, ECC: yes, 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.6451564 -------- -------- --- Thank You --- -------- -------- GPU-aware MPI detected, but by default GROMACS will not make use the direct GPU communication capabilities of MPI. For improved performance try enabling the feature by setting the GMX_ENABLE_DIRECT_GPU_COMM environment variable. Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 500000000 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 1 bd-fric = 0 ld-seed = 1866149285 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 1000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 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 = 56 fourier-ny = 56 fourier-nz = 80 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 3d epsilon-surface = 0 tcoupl = Nose-Hoover nsttcouple = 10 nh-chain-length = 1 print-nose-hoover-chain-variables = false pcoupl = Parrinello-Rahman pcoupltype = Isotropic nstpcouple = 10 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 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 = 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: 2683.92 93819.1 ref-t: 298 298 tau-t: 1 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 1.321 When checking whether update groups are usable: At least one moleculetype does not conform to the requirements for using update groups