:-) GROMACS - gmx mdrun, 2021 (-: 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 Gilles Gouaillardet 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 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/pb/Desktop/PDMS-isop-ryzen Process ID: 2690 Command line: gmx mdrun -deffnm SR.isop.npt.iso -bonded gpu -nb gpu -pme gpu -ntomp 4 -ntmpi 16 -npme 1 GROMACS version: 2021 Verified release checksum is 3e06a5865d6ff726fc417dea8d55afd37ac3cbb94c02c54c76d7a881c49c5dd8 Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: CUDA SIMD instructions: AVX2_256 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/gcc-9 GNU 9.3.0 C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -pthread -O3 -DNDEBUG C++ compiler: /usr/bin/g++-9 GNU 9.3.0 C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -pthread -fopenmp -O3 -DNDEBUG CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2021 NVIDIA Corporation;Built on Thu_Jan_28_19:32:09_PST_2021;Cuda compilation tools, release 11.2, V11.2.142;Build cuda_11.2.r11.2/compiler.29558016_0 CUDA compiler flags:-std=c++17;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-Wno-deprecated-gpu-targets;-gencode;arch=compute_35,code=compute_35;-gencode;arch=compute_50,code=compute_50;-gencode;arch=compute_52,code=compute_52;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-gencode;arch=compute_70,code=compute_70;-gencode;arch=compute_75,code=compute_75;-gencode;arch=compute_80,code=compute_80;-use_fast_math;-D_FORCE_INLINES;-mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -pthread -fopenmp -O3 -DNDEBUG CUDA driver: 11.20 CUDA runtime: 11.20 Running on 1 node with total 32 cores, 64 logical cores, 2 compatible GPUs Hardware detected: CPU info: Vendor: AMD Brand: AMD Ryzen Threadripper 3970X 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 Sockets, cores, and logical processors: Socket 0: [ 0 32] [ 1 33] [ 2 34] [ 3 35] [ 4 36] [ 5 37] [ 6 38] [ 7 39] [ 8 40] [ 9 41] [ 10 42] [ 11 43] [ 12 44] [ 13 45] [ 14 46] [ 15 47] [ 16 48] [ 17 49] [ 18 50] [ 19 51] [ 20 52] [ 21 53] [ 22 54] [ 23 55] [ 24 56] [ 25 57] [ 26 58] [ 27 59] [ 28 60] [ 29 61] [ 30 62] [ 31 63] GPU info: Number of GPUs detected: 2 #0: NVIDIA GeForce RTX 3090, compute cap.: 8.6, ECC: no, stat: compatible #1: 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.4457626 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 10000000 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -1010638898 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 50000 nstvout = 50000 nstfout = 0 nstlog = 50000 nstcalcenergy = 100 nstenergy = 50000 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 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 = 0.16 fourier-nx = 160 fourier-ny = 160 fourier-nz = 96 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 = 10 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = Berendsen 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]= 3.18755e-01 posres-com[1]= 3.63250e-01 posres-com[2]= 1.66954e-01 posres-comB (3): posres-comB[0]= 3.18755e-01 posres-comB[1]= 3.63250e-01 posres-comB[2]= 1.66954e-01 QMMM = false qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = true Shake-SOR = false shake-tol = 0.0001 lincs-order = 4 lincs-iter = 2 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 grpopts: nrdf: 177838 159999 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 10 to 100, rlist from 1 to 1 Initializing Domain Decomposition on 16 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.791 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.449 nm, LJ-14, atoms 28926 28929 multi-body bonded interactions: 0.448 nm, Proper Dih., atoms 64987 64992 Minimum cell size due to bonded interactions: 0.493 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.220 nm Estimated maximum distance required for P-LINCS: 0.220 nm 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 0.989 nm The maximum allowed number of cells is: X 25 Y 24 Z 15 Domain decomposition grid 5 x 3 x 1, 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: X 1 Y 1 The initial domain decomposition cell size is: X 5.00 nm Y 8.00 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.000 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.000 nm multi-body bonded interactions (-rdd) 1.000 nm atoms separated by up to 5 constraints (-rcon) 5.000 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 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: X 0.20 Y 0.12 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 AORUS 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 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 16 MPI threads Using 4 OpenMP threads per tMPI thread Pinning threads with an auto-selected logical core stride of 1 System total charge: 3.776 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.: 1.6097e-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 0.135 nm, rlist 1.135 nm Using full Lennard-Jones parameter combination matrix 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 64640 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 10 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: 134160 Atoms Atom distribution over 15 domains: av 8944 stddev 1862 min 5967 max 12551 NOTE: DLB will not turn on during the first phase of PME tuning Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest Started mdrun on rank 0 Wed Mar 10 11:11:57 2021 Step Time 0 0.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.14177e+05 3.78600e+04 6.36687e+05 7.58889e+04 7.47693e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.05136e+03 2.33662e+04 -2.79975e+07 -2.83814e+05 -1.33767e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.23494e+07 1.48439e+05 5.23379e-09 -1.47281e+07 4.21398e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.43067e+07 -1.43062e+07 3.00041e+02 -2.48798e+01 -1.20799e+03 Constr. rmsd 2.85755e-06 DD step 99 load imb.: force 16.0% pme mesh/force 0.884 NOTE: DLB can now turn on, when beneficial DD step 49999 load imb.: force 7.5% pme mesh/force 1.632 Step Time 50000 100.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.54927e+05 3.75572e+04 7.27336e+05 7.62381e+04 7.45184e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.95385e+03 5.51987e+04 -2.85915e+07 -2.81626e+05 -1.39403e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26565e+07 1.59138e+05 3.34512e+04 -1.48063e+07 4.22184e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.43841e+07 -1.43212e+07 3.00601e+02 -2.70030e+01 -2.14200e+01 Constr. rmsd 2.79901e-06 DD step 99999 load imb.: force 12.6% pme mesh/force 1.540 Step Time 100000 200.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.53929e+05 3.78422e+04 7.24413e+05 7.55856e+04 7.37984e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.00099e+03 5.61297e+04 -2.85926e+07 -2.82903e+05 -1.45513e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26578e+07 1.58778e+05 3.42968e+04 -1.48114e+07 4.21070e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.43904e+07 -1.43354e+07 2.99808e+02 -2.94028e+01 -3.29746e+00 Constr. rmsd 2.78592e-06 DD step 149999 load imb.: force 11.7% pme mesh/force 1.609 Step Time 150000 300.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.54717e+05 3.72108e+04 7.26422e+05 7.60553e+04 7.46191e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.93117e+03 5.70870e+04 -2.86018e+07 -2.84908e+05 -1.52641e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26595e+07 1.59370e+05 3.51531e+04 -1.48158e+07 4.22679e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.43931e+07 -1.43496e+07 3.00953e+02 -3.23317e+01 1.67345e+01 Constr. rmsd 2.76631e-06 DD step 199999 load imb.: force 15.5% pme mesh/force 1.463 Step Time 200000 400.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.54403e+05 3.82327e+04 7.22909e+05 7.60696e+04 7.43804e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.95685e+03 5.63837e+04 -2.85939e+07 -2.87780e+05 -1.62584e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26552e+07 1.59657e+05 3.48307e+04 -1.48199e+07 4.18750e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44012e+07 -1.43641e+07 2.98156e+02 -3.66498e+01 -3.14150e+01 Constr. rmsd 2.74853e-06 DD step 249999 load imb.: force 18.2% pme mesh/force 1.535 Step Time 250000 500.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.53313e+05 3.80186e+04 7.27412e+05 7.55403e+04 7.41184e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.96016e+03 5.62041e+04 -2.86028e+07 -2.91159e+05 -1.74893e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26594e+07 1.60105e+05 3.56619e+04 -1.48257e+07 4.21045e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44047e+07 -1.43795e+07 2.99790e+02 -4.23701e+01 -6.13216e+01 Constr. rmsd 2.69995e-06 DD step 299999 load imb.: force 18.0% pme mesh/force 1.488 Step Time 300000 600.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.53571e+05 3.76878e+04 7.27032e+05 7.64116e+04 7.41056e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.09053e+03 5.73519e+04 -2.86073e+07 -2.93785e+05 -1.91881e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26610e+07 1.60249e+05 3.59105e+04 -1.48310e+07 4.21193e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44098e+07 -1.43952e+07 2.99896e+02 -5.09451e+01 -5.72683e+01 Constr. rmsd 2.64360e-06 DD step 349999 load imb.: force 18.9% pme mesh/force 1.464 Step Time 350000 700.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.55581e+05 3.74852e+04 7.28257e+05 7.61617e+04 7.39994e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.97874e+03 5.88052e+04 -2.86166e+07 -2.98471e+05 -2.09192e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26696e+07 1.59905e+05 3.61680e+04 -1.48340e+07 4.22974e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44110e+07 -1.44116e+07 3.01164e+02 -6.04965e+01 7.97576e+00 Constr. rmsd 2.59838e-06 DD step 399999 load imb.: force 16.8% pme mesh/force 1.478 Step Time 400000 800.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.53443e+05 3.75266e+04 7.25699e+05 7.57179e+04 7.37381e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.97729e+03 5.79322e+04 -2.86058e+07 -3.00218e+05 -2.18572e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26633e+07 1.59452e+05 3.60379e+04 -1.48391e+07 4.19219e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44199e+07 -1.44280e+07 2.98490e+02 -6.60140e+01 -3.12515e+01 Constr. rmsd 2.55408e-06 DD step 449999 load imb.: force 17.0% pme mesh/force 1.401 Step Time 450000 900.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.55409e+05 3.78093e+04 7.27238e+05 7.60679e+04 7.32174e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.94339e+03 5.78648e+04 -2.86136e+07 -3.01285e+05 -2.28962e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26657e+07 1.59483e+05 3.70633e+04 -1.48420e+07 4.20631e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44213e+07 -1.44450e+07 2.99495e+02 -7.24067e+01 1.47322e+01 Constr. rmsd 2.54085e-06 DD step 499999 load imb.: force 15.7% pme mesh/force 1.404 Step Time 500000 1000.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.53004e+05 3.79104e+04 7.28007e+05 7.57822e+04 7.33765e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.02672e+03 5.85750e+04 -2.86122e+07 -3.02693e+05 -2.36650e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26670e+07 1.59216e+05 3.70202e+04 -1.48427e+07 4.21992e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44207e+07 -1.44620e+07 3.00464e+02 -7.73276e+01 1.44020e+01 Constr. rmsd 2.52850e-06 DD step 549999 load imb.: force 14.5% pme mesh/force 1.497 Step Time 550000 1100.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.55331e+05 3.77960e+04 7.24375e+05 7.58238e+04 7.36290e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.87057e+03 5.82504e+04 -2.86109e+07 -3.04041e+05 -2.43946e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26646e+07 1.59474e+05 3.78650e+04 -1.48464e+07 4.18318e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44281e+07 -1.44788e+07 2.97848e+02 -8.21469e+01 -1.63354e+01 Constr. rmsd 2.52782e-06 DD step 599999 load imb.: force 16.1% pme mesh/force 1.377 Step Time 600000 1200.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.55318e+05 3.72667e+04 7.28584e+05 7.61782e+04 7.35997e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.13399e+03 5.95213e+04 -2.86188e+07 -3.04531e+05 -2.51114e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26684e+07 1.59927e+05 3.79552e+04 -1.48456e+07 4.21026e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44246e+07 -1.44961e+07 2.99776e+02 -8.70235e+01 5.29517e+01 Constr. rmsd 2.52829e-06 DD step 649999 load imb.: force 16.0% pme mesh/force 1.445 Step Time 650000 1300.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.55039e+05 3.71800e+04 7.29642e+05 7.66887e+04 7.41061e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.00536e+03 5.97135e+04 -2.86260e+07 -3.03295e+05 -2.55530e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26716e+07 1.60376e+05 3.89701e+04 -1.48455e+07 4.20857e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44246e+07 -1.45133e+07 2.99656e+02 -9.00974e+01 5.52067e+01 Constr. rmsd 2.48732e-06 DD step 699999 load imb.: force 14.9% pme mesh/force 1.449 Step Time 700000 1400.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.53778e+05 3.76918e+04 7.30638e+05 7.49502e+04 7.35583e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.95438e+03 6.05699e+04 -2.86287e+07 -3.05475e+05 -2.61594e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26722e+07 1.60327e+05 3.94005e+04 -1.48513e+07 4.20694e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44306e+07 -1.45306e+07 2.99540e+02 -9.44061e+01 -1.18782e+01 Constr. rmsd 2.48797e-06 DD step 749999 load imb.: force 14.7% pme mesh/force 1.457 Step Time 750000 1500.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.53566e+05 3.81557e+04 7.29912e+05 7.58702e+04 7.36685e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.10698e+03 5.99812e+04 -2.86278e+07 -3.05391e+05 -2.65374e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26737e+07 1.60369e+05 3.97042e+04 -1.48486e+07 4.22574e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44261e+07 -1.45479e+07 3.00878e+02 -9.71424e+01 -4.03127e+01 Constr. rmsd 2.48253e-06 DD step 799999 load imb.: force 17.0% pme mesh/force 1.526 Step Time 800000 1600.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.54651e+05 3.80118e+04 7.33094e+05 7.65453e+04 7.35924e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.00847e+03 6.06493e+04 -2.86360e+07 -3.05592e+05 -2.67590e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26757e+07 1.60628e+05 4.00714e+04 -1.48493e+07 4.20605e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44287e+07 -1.45652e+07 2.99477e+02 -9.87649e+01 -4.15458e+01 Constr. rmsd 2.47638e-06 Writing checkpoint, step 848000 at Wed Mar 10 11:26:57 2021 DD step 849999 load imb.: force 16.6% pme mesh/force 1.413 Step Time 850000 1700.00000 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.57160e+05 3.72577e+04 7.32623e+05 7.60871e+04 7.29520e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.06640e+03 6.02740e+04 -2.86387e+07 -3.05556e+05 -2.69562e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26782e+07 1.60124e+05 3.99512e+04 -1.48505e+07 4.21339e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44292e+07 -1.45828e+07 2.99999e+02 -1.00220e+02 7.31452e+01 Constr. rmsd 2.48436e-06 Received the INT signal, stopping within 100 steps Step Time 887700 1775.40000 Writing checkpoint, step 887700 at Wed Mar 10 11:27:40 2021 Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.53251e+05 3.75349e+04 7.31074e+05 7.60057e+04 7.29641e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.92294e+03 6.11912e+04 -2.86359e+07 -3.05844e+05 -2.70675e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26767e+07 1.60045e+05 4.01208e+04 -1.48540e+07 4.21941e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44321e+07 -1.45961e+07 3.00428e+02 -1.01046e+02 3.08498e+01 Constr. rmsd 2.47986e-06 Energy conservation over simulation part #1 of length 1775.4 ns, time 0 to 1775.4 ns Conserved energy drift: -1.22e-03 kJ/mol/ps per atom <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 887701 steps using 8878 frames Energies (kJ/mol) Bond G96Bond Angle G96Angle Proper Dih. 2.53969e+05 3.78022e+04 7.27604e+05 7.58445e+04 7.38788e+04 Improper Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 6.00136e+03 5.81955e+04 -2.86114e+07 -2.97182e+05 -2.14646e+04 Coulomb (SR) Coul. recip. Position Rest. Potential Kinetic En. 1.26650e+07 1.59805e+05 3.68223e+04 -1.48351e+07 4.21323e+05 Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) -1.44138e+07 -1.44457e+07 2.99988e+02 -6.66306e+01 -1.74184e+01 Constr. rmsd 0.00000e+00 Box-X Box-Y Box-Z 2.16248e+01 2.07598e+01 1.29749e+01 Total Virial (kJ/mol) 1.34365e+05 -8.06140e+03 -4.69171e+01 -8.06139e+03 1.44411e+05 7.15888e+01 -4.69208e+01 7.15809e+01 1.52674e+05 Pressure (bar) 2.02292e+01 5.01163e+01 -2.96835e-01 5.01162e+01 -9.41582e+00 -3.70492e-01 -2.96802e-01 -3.70430e-01 -6.30686e+01 T-PDMS T-ISOP 3.00004e+02 2.99970e+02 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- Pair Search distance check 71158.016784 640422.151 0.0 NxN Ewald Elec. + LJ [F] 69638390.350848 4596133763.156 96.9 NxN Ewald Elec. + LJ [V&F] 703498.629312 75274353.336 1.6 1,4 nonbonded interactions 184286.727600 16585805.484 0.3 Reset In Box 1190.938320 3572.815 0.0 CG-CoM 1191.072480 3573.217 0.0 Bonds 52764.947440 3113131.899 0.1 Angles 187056.354720 31425467.593 0.7 Propers 35010.927440 8017502.384 0.2 Impropers 8877.010000 1846418.080 0.0 Pos. Restr. 1278.289440 63914.472 0.0 Virial 11969.437785 215449.880 0.0 Stop-CM 1191.072480 11910.725 0.0 P-Coupling 11909.517360 71457.104 0.0 Calc-Ekin 23819.034720 643113.937 0.0 Lincs 59858.282599 3591496.956 0.1 Lincs-Mat 500927.727240 2003710.909 0.0 Constraint-V 119716.565198 1077449.087 0.0 Constraint-Vir 5985.889279 143661.343 0.0 ----------------------------------------------------------------------------- Total 4740866174.528 100.0 ----------------------------------------------------------------------------- D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 54102.3 av. #atoms communicated per step for LINCS: 3 x 4009.9 Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 15.2%. The balanceable part of the MD step is 69%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 10.4%. Average PME mesh/force load: 1.466 Part of the total run time spent waiting due to PP/PME imbalance: 15.1 % NOTE: 10.4 % of the available CPU time was lost due to load imbalance in the domain decomposition. You might want to use dynamic load balancing (option -dlb.) You can also consider manually changing the decomposition (option -dd); e.g. by using fewer domains along the box dimension in which there is considerable inhomogeneity in the simulated system. NOTE: 15.1 % performance was lost because the PME ranks had more work to do than the PP ranks. You might want to increase the number of PME ranks or increase the cut-off and the grid spacing. R E A L C Y C L E A N D T I M E A C C O U N T I N G On 15 MPI ranks doing PP, each using 4 OpenMP threads, and on 1 MPI rank doing PME, using 4 OpenMP threads Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Domain decomp. 15 4 8877 30.664 6807.665 3.0 DD comm. load 15 4 90 0.005 1.194 0.0 Send X to PME 15 4 887701 44.811 9948.180 4.5 Neighbor search 15 4 8878 10.910 2421.981 1.1 Launch GPU ops. 15 4 1775402 214.598 47641.799 21.3 Comm. coord. 15 4 878823 127.533 28312.884 12.7 Force 15 4 887701 80.316 17830.595 8.0 Wait + Comm. F 15 4 887701 149.745 33244.072 14.9 PME mesh * 1 4 887701 498.109 7372.184 3.3 PME wait for PP * 445.012 6586.335 2.9 Wait + Recv. PME F 15 4 887701 43.019 9550.345 4.3 Wait PME GPU gather 15 4 887701 24.818 5509.749 2.5 Wait Bonded GPU 15 4 8878 0.008 1.719 0.0 Wait GPU NB nonloc. 15 4 887701 12.810 2843.947 1.3 Wait GPU NB local 15 4 887701 3.719 825.545 0.4 NB X/F buffer ops. 15 4 3533048 36.458 8093.771 3.6 Write traj. 15 4 20 0.046 10.252 0.0 Update 15 4 887701 39.640 8800.301 3.9 Constraints 15 4 887701 136.987 30411.910 13.6 Comm. energies 15 4 88771 8.169 1813.659 0.8 ----------------------------------------------------------------------------- Total 943.124 223337.040 100.0 ----------------------------------------------------------------------------- (*) Note that with separate PME ranks, the walltime column actually sums to twice the total reported, but the cycle count total and % are correct. ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 60359.682 943.124 6400.0 (ns/day) (hour/ns) Performance: 162.645 0.148 Finished mdrun on rank 0 Wed Mar 10 11:27:40 2021