:-) GROMACS - gmx mdrun, 2021-beta1-UNCHECKED (-: GROMACS is written by: Andrey Alekseenko 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 Artem Zhmurov 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) 2001-2019, 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 2021-beta1-UNCHECKED Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/pb/Desktop/PE-PVP-ISOP-EGDMA- TA Process ID: 123495 Command line: gmx mdrun -deffnm PE.sys.LB.nvt -nb gpu -pme gpu -ntomp 4 -ntmpi 16 -npme 1 -nsteps 100000 GROMACS version: 2021-beta1-UNCHECKED Verified release checksum is NotSourceDistribution Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: CUDA SIMD instructions: AVX2_128 FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128 RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /usr/bin/cc GNU 7.5.0 C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -pthread -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 7.5.0 C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -pthread -fopenmp -O3 -DNDEBUG CUDA compiler: /usr/local/cuda-11.1/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2020 NVIDIA Corporation;Built on Tue_Sep_15_19:10:02_PDT_2020;Cuda compilation tools, release 11.1, V11.1.74;Build cuda_11.1.TC455_06.29069683_0 CUDA compiler flags:-gencode;arch=compute_75,code=sm_75;-use_fast_math;-D_FORCE_INLINES;-mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -pthread -fopenmp -O3 -DNDEBUG CUDA driver: 11.10 CUDA runtime: 11.10 Running on 1 node with total 32 cores, 64 logical cores, 2 compatible GPUs Hardware detected: CPU info: Vendor: AMD Brand: AMD Ryzen Threadripper 2990WX 32-Core Processor Family: 23 Model: 8 Stepping: 2 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 Sockets, cores, and logical processors: Socket 0: [ 0 1] [ 2 3] [ 4 5] [ 6 7] [ 8 9] [ 10 11] [ 12 13] [ 14 15] [ 32 33] [ 34 35] [ 36 37] [ 38 39] [ 40 41] [ 42 43] [ 44 45] [ 46 47] [ 16 17] [ 18 19] [ 20 21] [ 22 23] [ 24 25] [ 26 27] [ 28 29] [ 30 31] [ 48 49] [ 50 51] [ 52 53] [ 54 55] [ 56 57] [ 58 59] [ 60 61] [ 62 63] GPU info: Number of GPUs detected: 2 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.: 7.5, ECC: no, stat: compatible #1: NVIDIA GeForce RTX 2080 Ti, compute cap.: 7.5, 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 --- -------- -------- The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 4 (and the command-line setting agreed with that) Enabling GPU buffer operations required by GMX_GPU_DD_COMMS (equivalent with GMX_USE_GPU_BUFFER_OPS=1). This run has requested the 'GPU halo exchange' feature, enabled by the GMX_GPU_DD_COMMS environment variable. This run uses the 'GPU PME-PP communications' feature, enabled by the GMX_GPU_PME_PP_COMMS environment variable. Input Parameters: integrator = sd tinit = 0 dt = 0.001 nsteps = 500000 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -436869696 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstcalcenergy = 100 nstenergy = 5000 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 100 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 1 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.416 fourier-nx = 36 fourier-ny = 72 fourier-nz = 2560 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 tcoupl = No nsttcouple = -1 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 grpopts: nrdf: 63203 19599.7 24399.6 27099.6 64999 ref-t: 310 360 360 360 360 tau-t: 0.1 0.1 0.1 0.1 0.1 annealing: No No No No No annealing-npoints: 0 0 0 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 The -nsteps functionality is deprecated, and may be removed in a future version. Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field. Overriding nsteps with value passed on the command line: 100000 steps, 100 ps Initializing Domain Decomposition on 16 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.514 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.414 nm, LJ-14, atoms 50463 50466 multi-body bonded interactions: 0.414 nm, Proper Dih., atoms 50463 50466 Minimum cell size due to bonded interactions: 0.455 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.774 nm Estimated maximum distance required for P-LINCS: 0.774 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Using 1 separate PME ranks Optimizing the DD grid for 15 cells with a minimum initial size of 0.967 nm The maximum allowed number of cells is: X 14 Y 28 Z 1033 Domain decomposition grid 1 x 1 x 15, 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 66.67 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.000 nm two-body bonded interactions (-rdd) 1.000 nm multi-body bonded interactions (-rdd) 1.000 nm atoms separated by up to 5 constraints (-rcon) 14.200 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 1.000 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: Z 0.02 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.000 nm two-body bonded interactions (-rdd) 1.000 nm multi-body bonded interactions (-rdd) 1.000 nm atoms separated by up to 5 constraints (-rcon) 1.000 nm On host TR1 2 GPUs selected for this run. Mapping of GPU IDs to the 16 GPU tasks in the 16 ranks on this node: PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PME:1 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU PME tasks will do all aspects on the GPU Using 16 MPI threads Using 4 OpenMP threads per tMPI thread Note: Peer access enabled between the following GPU pairs in the node: 0->1 1->0 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 0.320163 nm for Ewald Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05 Initialized non-bonded Ewald tables, spacing: 9.33e-04 size: 1073 Generated table with 1000 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ12. Tabscale = 500 points/nm Long Range LJ corr.: 4.0128e-03 Using GPU 8x8 nonbonded short-range kernels Using a 8x8 pair-list setup: updated every 100 steps, buffer 0.000 nm, rlist 1.000 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 1.000 nm Using full Lennard-Jones parameter combination matrix Removing pbc first time 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 92788 There are constraints between atoms in different decomposition domains, will communicate selected coordinates each lincs iteration Linking all bonded interactions to atoms Intra-simulation communication will occur every 100 steps. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ N. Goga and A. J. Rzepiela and A. H. de Vries and S. J. Marrink and H. J. C. Berendsen Efficient Algorithms for Langevin and DPD Dynamics J. Chem. Theory Comput. 8 (2012) pp. 3637--3649 -------- -------- --- Thank You --- -------- --------