Log file opened on Fri Aug 4 10:14:55 2023 Host: node971 pid: 156909 rank ID: 0 number of ranks: 640 :-) GROMACS - gmx mdrun, 2018.4 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf 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) 2001-2017, 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 2018.4 Executable: /home/software/gromacs/2018.4/bin/gmx_mpi Data prefix: /home/software/gromacs/2018.4 Working dir: /home/istewart/8.2nvt Command line: gmx_mpi mdrun -s topol.tpr -v -o trajectory GROMACS version: 2018.4 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX_256 FFT library: fftw-3.3.3-sse2 RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled Built on: 2018-12-14 15:25:09 Built by: lgardner462@node028.cm.cluster [CMAKE] Build OS/arch: Linux 3.10.0-514.26.2.el7.x86_64 x86_64 Build CPU vendor: Intel Build CPU brand: Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /bin/cc GNU 4.8.5 C compiler flags: -mavx -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /bin/c++ GNU 4.8.5 C++ compiler flags: -mavx -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast Running on 20 nodes with total 640 cores, 640 logical cores Cores per node: 32 Logical cores per node: 32 Hardware detected on host node971 (the node of MPI rank 0): CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) Gold 6130 CPU @ 2.10GHz Family: 6 Model: 85 Stepping: 4 Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl 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: Cannot run AVX-512 detection - assuming 2 Hardware topology: Basic Sockets, cores, and logical processors: Socket 0: [ 0] [ 4] [ 8] [ 12] [ 14] [ 10] [ 6] [ 2] [ 16] [ 20] [ 24] [ 28] [ 30] [ 26] [ 22] [ 18] Socket 1: [ 1] [ 5] [ 9] [ 13] [ 15] [ 11] [ 7] [ 3] [ 17] [ 21] [ 25] [ 29] [ 31] [ 27] [ 23] [ 19] Highest SIMD level requested by all nodes in run: AVX_512 SIMD instructions selected at compile time: AVX_256 This program was compiled for different hardware than you are running on, which could influence performance. ++++ 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 1 Input Parameters: integrator = md tinit = 0 dt = 0.001 nsteps = 100000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 1170566482 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 5000 nstcalcenergy = 100 nstenergy = 5000 nstxout-compressed = 5000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 100 ns-type = Grid pbc = xyz periodic-molecules = true verlet-buffer-tolerance = 0.005 rlist = 1.487 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 fourier-nx = 84 fourier-ny = 84 fourier-nz = 112 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 implicit-solvent = No gb-algorithm = Still nstgbradii = 1 rgbradii = 1 gb-epsilon-solvent = 80 gb-saltconc = 0 gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation sa-surface-tension = 2.05016 tcoupl = V-rescale nsttcouple = 100 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = No pcoupltype = Anisotropic nstpcouple = -1 tau-p = 5 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 QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 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 grpopts: nrdf: 93329 2240.98 181117 ref-t: 303 303 303 tau-t: 1 1 1 annealing: No No No annealing-npoints: 0 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Initializing Domain Decomposition on 640 ranks Dynamic load balancing: off Minimum cell size due to atom displacement: 0.467 nm NOTE: Periodic molecules are present in this system. Because of this, the domain decomposition algorithm cannot easily determine the minimum cell size that it requires for treating bonded interactions. Instead, domain decomposition will assume that half the non-bonded cut-off will be a suitable lower bound. Minimum cell size due to bonded interactions: 0.743 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 Guess for relative PME load: 0.10 Will use 576 particle-particle and 64 PME only ranks This is a guess, check the performance at the end of the log file Using 64 separate PME ranks, as guessed by mdrun Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 576 cells with a minimum initial size of 0.929 nm The maximum allowed number of cells is: X 10 Y 10 Z 13 Domain decomposition grid 8 x 8 x 9, separate PME ranks 64 PME domain decomposition: 8 x 8 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 2 Y 2 Z 2 The initial domain decomposition cell size is: X 1.26 nm Y 1.22 nm Z 1.44 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.487 nm two-body bonded interactions (-rdd) 1.487 nm multi-body bonded interactions (-rdd) 1.218 nm atoms separated by up to 5 constraints (-rcon) 1.218 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 2 Y 2 Z 2 The minimum size for domain decomposition cells is 0.743 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.59 Y 0.61 Z 0.51 The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.487 nm two-body bonded interactions (-rdd) 1.487 nm multi-body bonded interactions (-rdd) 0.743 nm atoms separated by up to 5 constraints (-rcon) 0.743 nm Using two step summing over 20 groups of on average 28.8 ranks Using 640 MPI processes Using 1 OpenMP thread per MPI process Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity System total charge: 0.002 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 0.448228 nm for Ewald Potential shift: LJ r^-12: -1.764e-02 r^-6: -1.328e-01, Ewald -7.143e-06 Initialized non-bonded Ewald correction tables, spacing: 1.10e-03 size: 1270 Long Range LJ corr.: 8.0873e-04 Generated table with 1243 data points for Ewald. Tabscale = 500 points/nm Generated table with 1243 data points for LJ6. Tabscale = 500 points/nm Generated table with 1243 data points for LJ12. Tabscale = 500 points/nm Generated table with 1243 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1243 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1243 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SIMD 4x4 nonbonded short-range kernels Using a dual 4x4 pair-list setup updated with dynamic pruning: outer list: updated every 100 steps, buffer 0.087 nm, rlist 1.487 nm inner list: updated every 22 steps, buffer 0.001 nm, rlist 1.401 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 100 steps, buffer 0.210 nm, rlist 1.610 nm inner list: updated every 22 steps, buffer 0.042 nm, rlist 1.442 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 729 There are inter charge-group constraints, 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 --- -------- -------- Linking all bonded interactions to atoms Intra-simulation communication will occur every 100 steps. Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: System ++++ 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: 122482 Atoms Atom distribution over 576 domains: av 212 stddev 20 min 164 max 247 Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 0.00e+00 Initial temperature: 302.633 K Started mdrun on rank 0 Fri Aug 4 10:15:07 2023 Step Time 0 0.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.49112e+06 4.68870e+02 1.74234e+03 3.00097e+03 1.27529e+01 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.52245e+02 5.80993e+02 2.01498e+04 1.53007e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.23758e+07 1.30622e+04 6.54221e+07 3.48347e+05 6.57704e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57704e+07 3.02845e+02 -1.89444e+02 7.43525e+04 2.10766e-06 DD step 99 load imb.: force 21.3% pme mesh/force 2.010 step 400: timed with pme grid 84 84 112, coulomb cutoff 1.400: 192.7 M-cycles step 600: timed with pme grid 80 72 96, coulomb cutoff 1.580: 231.3 M-cycles step 800: timed with pme grid 80 80 100, coulomb cutoff 1.517: 248.3 M-cycles step 1000: timed with pme grid 80 80 104, coulomb cutoff 1.467: 197.8 M-cycles step 1200: timed with pme grid 84 80 104, coulomb cutoff 1.458: 195.1 M-cycles step 1400: timed with pme grid 84 80 108, coulomb cutoff 1.421: 283.5 M-cycles step 1600: timed with pme grid 84 84 108, coulomb cutoff 1.404: 180.0 M-cycles step 1800: timed with pme grid 84 84 112, coulomb cutoff 1.400: 195.0 M-cycles optimal pme grid 84 84 108, coulomb cutoff 1.404 DD step 4999 load imb.: force 19.7% pme mesh/force 1.023 Step Time 5000 5.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61188e+06 9.26698e+02 3.10242e+03 3.20813e+03 1.06821e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 5.32469e+02 6.39528e+02 2.01464e+04 1.55430e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24652e+07 1.19598e+04 6.56575e+07 3.37590e+05 6.59951e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57723e+07 2.93492e+02 -1.89444e+02 6.85314e+04 2.10881e-06 DD step 9999 load imb.: force 19.4% pme mesh/force 1.041 Step Time 10000 10.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.60656e+06 8.43863e+02 3.27247e+03 3.15229e+03 1.02046e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 4.17726e+02 6.30219e+02 2.01262e+04 1.55800e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24746e+07 1.19861e+04 6.56652e+07 3.46348e+05 6.60115e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57723e+07 3.01106e+02 -1.89444e+02 6.98674e+04 2.09491e-06 DD step 14999 load imb.: force 20.4% pme mesh/force 1.060 Step Time 15000 15.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.60976e+06 9.28039e+02 3.26020e+03 3.19113e+03 7.38999e+01 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.79858e+02 6.31012e+02 2.02459e+04 1.55618e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24730e+07 1.19756e+04 6.56651e+07 3.47460e+05 6.60126e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57724e+07 3.02073e+02 -1.89444e+02 6.93463e+04 1.95156e-06 DD step 19999 load imb.: force 20.0% pme mesh/force 1.011 Step Time 20000 20.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.60953e+06 9.78728e+02 3.28569e+03 3.07499e+03 1.11445e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 4.20821e+02 6.84289e+02 2.02779e+04 1.55726e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24736e+07 1.20104e+04 6.56667e+07 3.48251e+05 6.60150e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57725e+07 3.02760e+02 -1.89444e+02 6.95468e+04 2.14567e-06 DD step 24999 load imb.: force 20.0% pme mesh/force 1.001 Step Time 25000 25.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61503e+06 8.62155e+02 3.31377e+03 3.10575e+03 1.08395e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.30299e+02 6.51061e+02 2.03995e+04 1.55589e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24685e+07 1.20657e+04 6.56657e+07 3.48851e+05 6.60146e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57725e+07 3.03283e+02 -1.89444e+02 6.87443e+04 2.09245e-06 DD step 29999 load imb.: force 19.3% pme mesh/force 1.012 Step Time 30000 30.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.60992e+06 8.62122e+02 3.40466e+03 2.99655e+03 1.06730e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.89185e+02 6.15650e+02 2.04156e+04 1.55716e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24724e+07 1.21213e+04 6.56658e+07 3.49015e+05 6.60149e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57726e+07 3.03425e+02 -1.89444e+02 6.93904e+04 2.04738e-06 DD step 34999 load imb.: force 17.4% pme mesh/force 1.036 Step Time 35000 35.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61515e+06 9.62497e+02 3.34633e+03 3.00081e+03 1.31270e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.79622e+02 6.28263e+02 2.03110e+04 1.55674e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24690e+07 1.21187e+04 6.56672e+07 3.49239e+05 6.60165e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57727e+07 3.03620e+02 -1.89444e+02 6.89039e+04 2.09224e-06 DD step 39999 load imb.: force 20.4% pme mesh/force 1.048 Step Time 40000 40.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61070e+06 8.97067e+02 3.36324e+03 2.97998e+03 7.53872e+01 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.73043e+02 6.27150e+02 2.03192e+04 1.55793e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24719e+07 1.23065e+04 6.56670e+07 3.46673e+05 6.60136e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57727e+07 3.01389e+02 -1.89444e+02 6.94373e+04 2.14916e-06 DD step 44999 load imb.: force 19.9% pme mesh/force 1.005 Step Time 45000 45.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61059e+06 8.99934e+02 3.25166e+03 3.11646e+03 1.21013e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.48694e+02 6.75599e+02 2.03592e+04 1.55608e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24703e+07 1.20343e+04 6.56633e+07 3.49550e+05 6.60128e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57727e+07 3.03890e+02 -1.89444e+02 6.91916e+04 2.04021e-06 DD step 49999 load imb.: force 18.7% pme mesh/force 1.029 Step Time 50000 50.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61315e+06 8.35207e+02 3.37737e+03 2.92193e+03 8.31505e+01 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.33450e+02 6.72099e+02 2.03724e+04 1.55652e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24692e+07 1.19088e+04 6.56649e+07 3.45363e+05 6.60102e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57728e+07 3.00250e+02 -1.89444e+02 6.89643e+04 2.05183e-06 DD step 54999 load imb.: force 18.1% pme mesh/force 1.003 Step Time 55000 55.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61234e+06 8.37012e+02 3.24901e+03 3.03977e+03 1.22015e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.49257e+02 6.41127e+02 2.04632e+04 1.55828e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24709e+07 1.21903e+04 6.56678e+07 3.49115e+05 6.60169e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57729e+07 3.03512e+02 -1.89444e+02 6.91976e+04 2.08372e-06 DD step 59999 load imb.: force 19.8% pme mesh/force 1.011 Step Time 60000 60.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61149e+06 8.53948e+02 3.27311e+03 2.99588e+03 8.75110e+01 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.84278e+02 6.52871e+02 2.04406e+04 1.55649e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24721e+07 1.20853e+04 6.56663e+07 3.48952e+05 6.60152e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57730e+07 3.03370e+02 -1.89444e+02 6.92182e+04 2.13556e-06 DD step 64999 load imb.: force 18.0% pme mesh/force 1.023 Step Time 65000 65.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.60760e+06 9.03566e+02 3.50984e+03 2.91204e+03 1.30723e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 2.70157e+02 6.77254e+02 2.04507e+04 1.55852e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24757e+07 1.19236e+04 6.56681e+07 3.47402e+05 6.60155e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57730e+07 3.02023e+02 -1.89444e+02 6.97815e+04 1.97476e-06 DD step 69999 load imb.: force 20.8% pme mesh/force 1.006 Step Time 70000 70.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61064e+06 8.33334e+02 3.27458e+03 2.99705e+03 8.78515e+01 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 2.70791e+02 7.03904e+02 2.05254e+04 1.55659e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24717e+07 1.22377e+04 6.56654e+07 3.48040e+05 6.60134e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57731e+07 3.02577e+02 -1.89444e+02 6.92844e+04 1.98178e-06 DD step 74999 load imb.: force 18.7% pme mesh/force 1.015 Step Time 75000 75.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61102e+06 9.30246e+02 3.24535e+03 2.99375e+03 1.17835e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 2.78448e+02 6.77439e+02 2.05243e+04 1.55555e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24734e+07 1.20557e+04 6.56662e+07 3.48749e+05 6.60150e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57731e+07 3.03194e+02 -1.89444e+02 6.92712e+04 2.01018e-06 DD step 79999 load imb.: force 19.5% pme mesh/force 1.005 Step Time 80000 80.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61641e+06 8.30447e+02 3.40307e+03 2.99968e+03 1.04377e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 2.76786e+02 6.66803e+02 2.04407e+04 1.55405e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24682e+07 1.19189e+04 6.56648e+07 3.47644e+05 6.60124e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57732e+07 3.02233e+02 -1.89444e+02 6.84725e+04 2.10101e-06 DD step 84999 load imb.: force 18.7% pme mesh/force 1.008 Step Time 85000 85.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61368e+06 9.73249e+02 3.29306e+03 3.00447e+03 9.52297e+01 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 2.56901e+02 6.57425e+02 2.03946e+04 1.55587e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24705e+07 1.21348e+04 6.56663e+07 3.49215e+05 6.60155e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57733e+07 3.03599e+02 -1.89444e+02 6.90169e+04 2.05441e-06 DD step 89999 load imb.: force 22.3% pme mesh/force 1.012 Step Time 90000 90.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61430e+06 8.35092e+02 3.40556e+03 2.89740e+03 1.13076e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.89955e+02 6.02818e+02 2.03310e+04 1.55432e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24705e+07 1.21124e+04 6.56653e+07 3.48682e+05 6.60140e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57733e+07 3.03136e+02 -1.89444e+02 6.88519e+04 2.11309e-06 DD step 94999 load imb.: force 19.4% pme mesh/force 0.998 Step Time 95000 95.00000 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61349e+06 8.53108e+02 3.35487e+03 2.92247e+03 1.09275e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.03197e+02 6.36703e+02 2.03866e+04 1.55508e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24693e+07 1.18873e+04 6.56638e+07 3.46767e+05 6.60106e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57734e+07 3.01470e+02 -1.89444e+02 6.88587e+04 2.04461e-06 DD step 99999 load imb.: force 19.1% pme mesh/force 1.006 Step Time 100000 100.00000 Writing checkpoint, step 100000 at Fri Aug 4 10:16:50 2023 Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.60760e+06 8.19044e+02 3.42146e+03 3.00879e+03 9.94797e+01 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.61416e+02 6.18094e+02 2.04164e+04 1.55789e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24748e+07 1.21692e+04 6.56666e+07 3.49415e+05 6.60161e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57735e+07 3.03773e+02 -1.89444e+02 6.97685e+04 2.00951e-06 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 100001 steps using 1001 frames Energies (kJ/mol) Bond Angle U-B Proper Dih. Improper Dih. 1.61030e+06 8.93728e+02 3.29465e+03 3.03064e+03 1.04382e+02 CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Disper. corr. 3.72963e+02 6.46386e+02 2.03701e+04 1.55637e+06 -1.45294e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy 6.24707e+07 1.20692e+04 6.56636e+07 3.45422e+05 6.60090e+07 Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 6.57728e+07 3.00302e+02 -1.89444e+02 6.92485e+04 0.00000e+00 Total Virial (kJ/mol) -2.41126e+06 -8.53442e+01 -2.60509e+02 -8.42300e+01 -5.22337e+06 2.40795e+02 -2.71861e+02 2.22791e+02 9.97323e+03 Pressure (bar) 6.58691e+04 2.15918e+00 7.39097e+00 2.13014e+00 1.39152e+05 -6.79532e+00 7.68688e+00 -6.32602e+00 2.72472e+03 T-H306 T-ProteinT-Water_and_ions 2.99778e+02 2.98684e+02 3.00591e+02 P P - P M E L O A D B A L A N C I N G PP/PME load balancing changed the cut-off and PME settings: particle-particle PME rcoulomb rlist grid spacing 1/beta initial 1.400 nm 1.401 nm 84 84 112 0.120 nm 0.448 nm final 1.404 nm 1.405 nm 84 84 108 0.120 nm 0.450 nm cost-ratio 1.01 0.96 (note that these numbers concern only part of the total PP and PME load) 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 81370.498798 732334.489 0.1 NxN Ewald Elec. + LJ [F] 13044597.202296 860943415.352 90.4 NxN Ewald Elec. + LJ [V&F] 131895.196056 14112785.978 1.5 NxN LJ [F] 81.598176 2692.740 0.0 NxN LJ [V&F] 0.824224 35.442 0.0 NxN Ewald Elec. [F] 697280.790888 42534128.244 4.5 NxN Ewald Elec. [V&F] 7050.376136 592231.595 0.1 1,4 nonbonded interactions 256.802568 23112.231 0.0 Calc Weights 36744.967446 1322818.828 0.1 Spread Q Bspline 783892.638848 1567785.278 0.2 Gather F Bspline 783892.638848 4703355.833 0.5 3D-FFT 2974358.754108 23794870.033 2.5 Solve PME 5639.608448 360934.941 0.0 Reset In Box 122.604482 367.813 0.0 CG-CoM 122.726964 368.181 0.0 Bonds 6099.060990 359844.598 0.0 Angles 30.600306 5140.851 0.0 Propers 298.202982 68288.483 0.0 Impropers 10.200102 2121.621 0.0 Virial 148.550402 2673.907 0.0 Stop-CM 122.726964 1227.270 0.0 Calc-Ekin 245.208964 6620.642 0.0 Lincs 83.250236 4995.014 0.0 Lincs-Mat 234.366024 937.464 0.0 Constraint-V 10944.784329 87558.275 0.0 Constraint-Vir 108.721873 2609.325 0.0 Settle 3592.797855 1160473.707 0.1 CMAP 6.600066 11220.112 0.0 Urey-Bradley 176.701767 32336.423 0.0 ----------------------------------------------------------------------------- Total 952437284.671 100.0 ----------------------------------------------------------------------------- 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 896099.8 av. #atoms communicated per step for LINCS: 2 x 18529.6 Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 19.0%. The balanceable part of the MD step is 72%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 13.7%. Average PME mesh/force load: 1.022 Part of the total run time spent waiting due to PP/PME imbalance: 1.8 % NOTE: 13.7 % 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.) 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 576 MPI ranks doing PP, and on 64 MPI ranks doing PME Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Domain decomp. 576 1 1001 1.601 1931.549 1.4 DD comm. load 576 1 984 0.007 8.569 0.0 Send X to PME 576 1 100001 0.363 438.527 0.3 Neighbor search 576 1 1001 1.156 1394.978 1.0 Comm. coord. 576 1 99000 7.445 8984.395 6.3 Force 576 1 100001 64.879 78293.765 55.1 Wait + Comm. F 576 1 100001 13.840 16701.500 11.8 PME mesh * 64 1 100001 88.597 11879.525 8.4 PME wait for PP * 17.353 2326.834 1.6 Wait + Recv. PME F 576 1 100001 5.631 6794.977 4.8 NB X/F buffer ops. 576 1 298001 1.309 1579.446 1.1 Write traj. 576 1 21 0.014 16.595 0.0 Update 576 1 100001 0.299 361.308 0.3 Constraints 576 1 100001 3.677 4437.731 3.1 Comm. energies 576 1 1001 5.556 6704.382 4.7 Rest 0.197 238.170 0.2 ----------------------------------------------------------------------------- Total 105.975 142095.434 100.0 ----------------------------------------------------------------------------- (*) Note that with separate PME ranks, the walltime column actually sums to twice the total reported, but the cycle count total and % are correct. ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME redist. X/F 64 1 200002 12.733 1707.317 1.2 PME spread 64 1 100001 16.332 2189.916 1.5 PME gather 64 1 100001 14.295 1916.745 1.3 PME 3D-FFT 64 1 200002 16.595 2225.198 1.6 PME 3D-FFT Comm. 64 1 400004 25.895 3472.101 2.4 PME solve Elec 64 1 100001 2.662 356.896 0.3 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 67823.695 105.975 64000.0 (ns/day) (hour/ns) Performance: 81.530 0.294 Finished mdrun on rank 0 Fri Aug 4 10:16:53 2023