:-) 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: /usr/local/bin/gmx Data prefix: /usr/local Working dir: /home/qoraj/Documents/CG_simulations/tutorial_protein_part1 (1)/tutorial_2/template Process ID: 111492 Command line: gmx mdrun -deffnm minimization-vac -v GROMACS version: 2023.1 Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) GPU support: disabled SIMD instructions: AVX2_256 CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128 GPU FFT library: none Multi-GPU FFT: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /usr/bin/cc GNU 11.3.0 C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 11.3.0 C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp BLAS library: Internal LAPACK library: Internal Running on 1 node with total 8 cores, 8 processing units Hardware detected on host qoraj-Yoga-Slim-7-14ARE05: CPU info: Vendor: AMD Brand: AMD Ryzen 7 4700U with Radeon Graphics Family: 23 Model: 96 Stepping: 1 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] CPU limit set by OS: -1 Recommended max number of threads: 8 ++++ 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 = steep tinit = 0 dt = 0.01 nsteps = 100 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -60043474 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 = 100 nstxout-compressed = 1000 compressed-x-precision = 100 cutoff-scheme = Verlet nstlist = 20 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.155 coulombtype = Reaction-Field coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.1 epsilon-r = 15 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 1.1 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 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 = not available ensemble-temperature = -1 tcoupl = No nsttcouple = -1 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 12 compressibility (3x3): compressibility[ 0]={ 3.00000e-04, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 3.00000e-04, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 3.00000e-04} 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 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: 904 ref-t: 0 tau-t: 0 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0