:-) GROMACS - gmx mdrun, 2021.4-Ubuntu-2021.4-2 (-: 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 2021.4-Ubuntu-2021.4-2 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /media/D/Kutatás/Smart University/Gromacs/equil Process ID: 8135 Command line: gmx mdrun -deffnm nvt GROMACS version: 2021.4-Ubuntu-2021.4-2 Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: SSE4.1 FFT library: fftw-3.3.8-sse2-avx RDTSCP usage: enabled TNG support: enabled Hwloc support: hwloc-2.5.0 Tracing support: disabled C compiler: /usr/bin/cc GNU 11.2.0 C compiler flags: -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 11.2.0 C++ compiler flags: -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG Running on 1 node with total 6 cores, 12 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz Family: 6 Model: 165 Stepping: 2 Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Hardware topology: Full, with devices Sockets, cores, and logical processors: Socket 0: [ 0 6] [ 1 7] [ 2 8] [ 3 9] [ 4 10] [ 5 11] Numa nodes: Node 0 (16667492352 bytes mem): 0 6 1 7 2 8 3 9 4 10 5 11 Latency: 0 0 1.00 Caches: L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways L2: 262144 bytes, linesize 64 bytes, assoc. 4, shared 2 ways L3: 12582912 bytes, linesize 64 bytes, assoc. 16, shared 12 ways PCI devices: 0000:01:00.0 Id: 10de:1f95 Class: 0x0300 Numa: 0 0000:00:14.3 Id: 8086:06f0 Class: 0x0280 Numa: 0 0000:00:17.0 Id: 8086:06d3 Class: 0x0106 Numa: 0 0000:06:00.0 Id: 2646:5017 Class: 0x0108 Numa: 0 0000:07:00.0 Id: 10ec:8168 Class: 0x0200 Numa: 0 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: SSE4.1 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 --- -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 50000 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -994459665 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 2500 nstvout = 2500 nstfout = 0 nstlog = 2500 nstcalcenergy = 100 nstenergy = 2500 nstxout-compressed = 0 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 = Force-switch rvdw-switch = 1 rvdw = 1.2 DispCorr = No table-extension = 1 fourierspacing = 0.16 fourier-nx = 48 fourier-ny = 48 fourier-nz = 48 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 = 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 shift-vector = transformation-matrix = grpopts: nrdf: 80470 ref-t: 298 tau-t: 1 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Changing nstlist from 10 to 80, rlist from 1.2 to 1.319 Using 1 MPI thread Using 12 OpenMP threads 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 0.384195 nm for Ewald Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06 Initialized non-bonded Ewald tables, spacing: 1.02e-03 size: 1176 Generated table with 1159 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1159 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1159 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 80 steps, buffer 0.119 nm, rlist 1.319 nm inner list: updated every 13 steps, buffer 0.002 nm, rlist 1.202 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 80 steps, buffer 0.263 nm, rlist 1.463 nm inner list: updated every 13 steps, buffer 0.051 nm, rlist 1.251 nm Removing pbc first time Initializing LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 -------- -------- --- Thank You --- -------- -------- The number of constraints is 959 ++++ 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 --- -------- -------- ++++ 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: 39732 Atoms Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest RMS relative constraint deviation after constraining: 2.64e-06 Initial temperature: 296.159 K Started mdrun on rank 0 Tue May 12 11:55:57 2026 Step Time 0 0.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 4.34910e+02 1.49351e+03 2.48874e+03 7.91248e+01 -9.27753e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.38761e+03 1.31874e+04 7.70520e+04 -7.09488e+05 1.76664e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 8.42869e-04 -6.12526e+05 9.91045e+04 -5.13421e+05 -5.13421e+05 Temperature Pressure (bar) Constr. rmsd 2.96248e+02 -4.67338e+03 2.64915e-06 Step Time 2500 5.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.61045e+03 4.16463e+03 2.74499e+03 2.73432e+02 -8.36331e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.42785e+03 1.29940e+04 7.79057e+04 -6.35104e+05 1.79126e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 4.84984e+02 -5.32543e+05 9.47120e+04 -4.37831e+05 -5.12594e+05 Temperature Pressure (bar) Constr. rmsd 2.83118e+02 -3.67406e+02 3.06603e-06 Step Time 5000 10.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.66156e+03 4.50536e+03 2.84702e+03 3.02844e+02 -8.79842e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.53213e+03 1.29278e+04 7.55623e+04 -6.23474e+05 1.83205e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.65139e+02 -5.22618e+05 9.84166e+04 -4.24201e+05 -5.12575e+05 Temperature Pressure (bar) Constr. rmsd 2.94191e+02 5.70679e+01 2.94479e-06 Step Time 7500 15.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.63233e+03 4.48207e+03 2.82615e+03 3.19817e+02 -8.72413e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.44616e+03 1.31934e+04 7.50348e+04 -6.22054e+05 1.89258e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 4.99707e+02 -5.21599e+05 9.90259e+04 -4.22573e+05 -5.12561e+05 Temperature Pressure (bar) Constr. rmsd 2.96013e+02 -3.48688e+01 2.97246e-06 Step Time 10000 20.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.61106e+03 4.41735e+03 2.81600e+03 3.21698e+02 -8.83804e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.43408e+03 1.29459e+04 7.34877e+04 -6.18726e+05 1.86245e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.29820e+02 -5.20184e+05 1.00209e+05 -4.19975e+05 -5.12563e+05 Temperature Pressure (bar) Constr. rmsd 2.99551e+02 -2.99425e+02 2.93435e-06 Step Time 12500 25.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.65863e+03 4.62161e+03 2.90187e+03 2.75456e+02 -8.80079e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.43719e+03 1.28734e+04 7.45349e+04 -6.20852e+05 2.01370e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.28137e+02 -5.20887e+05 1.00472e+05 -4.20415e+05 -5.12526e+05 Temperature Pressure (bar) Constr. rmsd 3.00336e+02 -1.28178e+02 2.68694e-06 Step Time 15000 30.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.61565e+03 4.43412e+03 2.88004e+03 3.05707e+02 -8.70784e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.48704e+03 1.30051e+04 7.46525e+04 -6.21651e+05 1.85583e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.72692e+02 -5.21713e+05 9.94325e+04 -4.22280e+05 -5.12510e+05 Temperature Pressure (bar) Constr. rmsd 2.97228e+02 -2.53547e+02 2.72062e-06 Step Time 17500 35.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.62378e+03 4.34900e+03 2.84348e+03 2.90993e+02 -8.90314e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.43578e+03 1.30186e+04 7.37406e+04 -6.19185e+05 1.91096e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.99359e+02 -5.20262e+05 9.90772e+04 -4.21185e+05 -5.12500e+05 Temperature Pressure (bar) Constr. rmsd 2.96166e+02 -3.67679e+02 2.81334e-06 Step Time 20000 40.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.54303e+03 4.69881e+03 2.90803e+03 3.26504e+02 -9.12984e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.50241e+03 1.29831e+04 7.34170e+04 -6.18746e+05 1.86861e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.75199e+02 -5.19837e+05 1.00582e+05 -4.19254e+05 -5.12462e+05 Temperature Pressure (bar) Constr. rmsd 3.00666e+02 -1.05287e+02 2.67713e-06 Step Time 22500 45.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.63201e+03 4.45704e+03 2.87007e+03 2.43092e+02 -8.98275e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.40829e+03 1.30579e+04 7.42526e+04 -6.21674e+05 1.85651e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.69740e+02 -5.22225e+05 9.99186e+04 -4.22306e+05 -5.12456e+05 Temperature Pressure (bar) Constr. rmsd 2.98681e+02 -5.21266e+02 2.68989e-06 Step Time 25000 50.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.62552e+03 4.36752e+03 2.87067e+03 2.73885e+02 -8.70010e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.51884e+03 1.31204e+04 7.30636e+04 -6.20452e+05 1.76522e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 6.19662e+02 -5.22096e+05 9.98595e+04 -4.22237e+05 -5.12446e+05 Temperature Pressure (bar) Constr. rmsd 2.98505e+02 -1.41783e+02 2.64979e-06 Step Time 27500 55.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.59501e+03 4.52509e+03 2.83921e+03 2.89490e+02 -8.80317e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.46365e+03 1.31918e+04 7.40854e+04 -6.20969e+05 1.91801e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.09488e+02 -5.21432e+05 9.98945e+04 -4.21538e+05 -5.12411e+05 Temperature Pressure (bar) Constr. rmsd 2.98609e+02 -1.92508e+02 3.11609e-06 Step Time 30000 60.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.57742e+03 4.48108e+03 2.86579e+03 2.70627e+02 -8.75572e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.59624e+03 1.32117e+04 7.52051e+04 -6.21729e+05 1.96804e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.29997e+02 -5.20899e+05 9.91948e+04 -4.21704e+05 -5.12401e+05 Temperature Pressure (bar) Constr. rmsd 2.96518e+02 -3.08777e+01 3.05311e-06 Step Time 32500 65.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.63720e+03 4.49046e+03 2.84545e+03 3.22852e+02 -8.69098e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.45727e+03 1.31378e+04 7.53095e+04 -6.21269e+05 1.77974e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.25668e+02 -5.20632e+05 1.00261e+05 -4.20371e+05 -5.12379e+05 Temperature Pressure (bar) Constr. rmsd 2.99706e+02 8.73275e+01 2.97613e-06 Step Time 35000 70.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.56280e+03 4.35426e+03 2.96719e+03 2.58588e+02 -9.02634e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.48353e+03 1.31500e+04 7.43260e+04 -6.19833e+05 1.87866e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.07811e+02 -5.20246e+05 1.00516e+05 -4.19730e+05 -5.12394e+05 Temperature Pressure (bar) Constr. rmsd 3.00469e+02 2.18306e+02 3.04681e-06 Step Time 37500 75.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.54312e+03 4.55832e+03 2.80702e+03 2.78537e+02 -8.79639e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.46756e+03 1.29999e+04 7.40198e+04 -6.20042e+05 1.88626e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 4.71331e+02 -5.20889e+05 9.95413e+04 -4.21348e+05 -5.12335e+05 Temperature Pressure (bar) Constr. rmsd 2.97553e+02 -2.27926e+02 2.67700e-06 Step Time 40000 80.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.60928e+03 4.54588e+03 2.86958e+03 2.61364e+02 -8.98957e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.49013e+03 1.28548e+04 7.38437e+04 -6.18392e+05 1.96009e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.03868e+02 -5.19353e+05 1.00481e+05 -4.18871e+05 -5.12349e+05 Temperature Pressure (bar) Constr. rmsd 3.00363e+02 -8.70609e+01 2.85407e-06 Step Time 42500 85.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.62176e+03 4.44660e+03 2.88739e+03 2.73103e+02 -8.88592e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.47494e+03 1.30976e+04 7.49741e+04 -6.20495e+05 1.88561e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.27149e+02 -5.20195e+05 1.00120e+05 -4.20076e+05 -5.12317e+05 Temperature Pressure (bar) Constr. rmsd 2.99282e+02 9.23772e+01 2.73016e-06 Step Time 45000 90.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.68997e+03 4.33137e+03 2.82964e+03 3.09631e+02 -8.84019e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.55245e+03 1.30099e+04 7.26503e+04 -6.17672e+05 1.94693e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 4.96416e+02 -5.19740e+05 1.00107e+05 -4.19633e+05 -5.12293e+05 Temperature Pressure (bar) Constr. rmsd 2.99245e+02 -1.88198e+02 2.73886e-06 Step Time 47500 95.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.62555e+03 4.39728e+03 2.98493e+03 2.96982e+02 -9.12766e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.41694e+03 1.29751e+04 7.48586e+04 -6.20837e+05 1.92036e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.04352e+02 -5.20769e+05 9.94554e+04 -4.21314e+05 -5.12263e+05 Temperature Pressure (bar) Constr. rmsd 2.97297e+02 -2.05370e+02 2.66856e-06 Step Time 50000 100.00000 Writing checkpoint, step 50000 at Tue May 12 12:06:02 2026 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.59520e+03 4.33594e+03 2.92481e+03 2.33708e+02 -8.96218e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.42689e+03 1.29755e+04 7.44069e+04 -6.20308e+05 1.85839e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.04430e+02 -5.20942e+05 9.95933e+04 -4.21349e+05 -5.12266e+05 Temperature Pressure (bar) Constr. rmsd 2.97709e+02 -2.95331e+02 2.80143e-06 Energy conservation over simulation part #1 of length 100 ns, time 0 to 100 ns Conserved energy drift: 2.91e-04 kJ/mol/ps per atom <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 50001 steps using 501 frames Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.60556e+03 4.38764e+03 2.87813e+03 2.85585e+02 -8.86107e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.47087e+03 1.30545e+04 7.44252e+04 -6.22236e+05 1.86948e+03 Position Rest. Potential Kinetic En. Total Energy Conserved En. 5.32102e+02 -5.22613e+05 9.87365e+04 -4.23877e+05 -5.12441e+05 Temperature Pressure (bar) Constr. rmsd 2.95148e+02 -2.50672e+02 0.00000e+00 Total Virial (kJ/mol) 3.60458e+04 -2.69148e+02 7.06521e+01 -2.69570e+02 3.59569e+04 1.08435e+02 7.02362e+01 1.08535e+02 3.59471e+04 Pressure (bar) -2.55529e+02 2.06890e+01 -4.59461e+00 2.07235e+01 -2.48256e+02 -1.06077e+01 -4.56066e+00 -1.06159e+01 -2.48232e+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 11690.208484 105211.876 0.1 NxN QSTab Elec. + LJ [F] 800251.161184 42413311.543 60.1 NxN QSTab Elec. + LJ [V&F] 8099.278144 656041.530 0.9 NxN QSTab Elec. [F] 706309.022320 24014506.759 34.0 NxN QSTab Elec. [V&F] 7148.583984 293091.943 0.4 1,4 nonbonded interactions 255.305106 22977.460 0.0 Calc Weights 5959.919196 214557.091 0.3 Spread Q Bspline 127144.942848 254289.886 0.4 Gather F Bspline 127144.942848 762869.657 1.1 3D-FFT 185299.305912 1482394.447 2.1 Solve PME 115.202304 7372.947 0.0 Shift-X 24.872232 149.233 0.0 Bonds 51.251025 3023.810 0.0 Propers 209.604192 47999.360 0.1 Impropers 17.450349 3629.673 0.0 Pos. Restr. 50.051001 2502.550 0.0 Virial 19.928277 358.709 0.0 Stop-CM 19.945464 199.455 0.0 Calc-Ekin 397.399464 10729.786 0.0 Lincs 47.952877 2877.173 0.0 Lincs-Mat 238.814328 955.257 0.0 Constraint-V 1984.179364 17857.614 0.0 Constraint-Vir 19.400223 465.605 0.0 Settle 629.437764 232891.973 0.3 CMAP 6.350127 10795.216 0.0 Urey-Bradley 177.353547 32455.699 0.0 ----------------------------------------------------------------------------- Total 70593516.252 100.0 ----------------------------------------------------------------------------- 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 1 MPI rank, each using 12 OpenMP threads Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Neighbor search 1 12 626 6.547 203.626 1.1 Force 1 12 50001 517.201 16087.023 85.5 PME mesh 1 12 50001 61.242 1904.879 10.1 NB X/F buffer ops. 1 12 99376 9.130 283.993 1.5 Write traj. 1 12 21 0.464 14.442 0.1 Update 1 12 50001 5.271 163.958 0.9 Constraints 1 12 50003 3.977 123.704 0.7 Rest 0.965 30.003 0.2 ----------------------------------------------------------------------------- Total 604.797 18811.627 100.0 ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME spread 1 12 50001 29.051 903.598 4.8 PME gather 1 12 50001 21.236 660.539 3.5 PME 3D-FFT 1 12 100002 9.420 293.015 1.6 PME solve Elec 1 12 50001 1.304 40.574 0.2 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 7257.566 604.797 1200.0 (ns/day) (hour/ns) Performance: 14.286 1.680 Finished mdrun on rank 0 Tue May 12 12:06:02 2026