:-) GROMACS - gmx mdrun, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: 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 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ubuntu/Home/Documents/7_semester/molmod/oving4_2 Process ID: 18777 Command line: gmx mdrun -v GROMACS version: 2020.1-Ubuntu-2020.1-1 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: SSE2 FFT library: fftw-3.3.8-sse2-avx RDTSCP usage: disabled TNG support: enabled Hwloc support: hwloc-2.1.0 Tracing support: disabled C compiler: /usr/bin/cc GNU 9.3.0 C compiler flags: -msse2 -fexcess-precision=fast -funroll-all-loops C++ compiler: /usr/bin/c++ GNU 9.3.0 C++ compiler flags: -msse2 -fexcess-precision=fast -funroll-all-loops -fopenmp Running on 1 node with total 1 cores, 1 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Core(TM) i5-3210M CPU @ 2.50GHz Family: 6 Model: 58 Stepping: 9 Features: aes apic avx clfsh cmov cx8 cx16 intel lahf mmx msr nonstop_tsc pcid pclmuldq popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 x2apic Hardware topology: Full, with devices Sockets, cores, and logical processors: Socket 0: [ 0] Numa nodes: Node 0 (1028964352 bytes mem): 0 Latency: 0 0 1.00 Caches: L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways L3: 3145728 bytes, linesize 64 bytes, assoc. 12, shared 1 ways PCI devices: 0000:00:02.0 Id: 80ee:beef Class: 0x0300 Numa: 0 0000:00:03.0 Id: 8086:100e Class: 0x0200 Numa: 0 0000:00:0d.0 Id: 8086:2829 Class: 0x0106 Numa: 0 Highest SIMD level requested by all nodes in run: AVX_256 SIMD instructions selected at compile time: SSE2 This program was compiled for different hardware than you are running on, which could influence performance. The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. ++++ 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 = 55000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -1641588220 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 100 nstvout = 50 nstfout = 0 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 0.9 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 0.9 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 0.9 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier-nx = 16 fourier-ny = 16 fourier-nz = 16 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 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 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: 1293 ref-t: 300 tau-t: 0.5 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Using 1 MPI thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread 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 0.288146 nm for Ewald Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-05 Initialized non-bonded Coulomb Ewald tables, spacing: 8.85e-04 size: 1018 Using SIMD 4x4 nonbonded short-range kernels Using a 4x4 pair-list setup: updated every 10 steps, buffer 0.000 nm, rlist 0.900 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: updated every 10 steps, buffer 0.037 nm, rlist 0.937 nm Using geometric Lennard-Jones combination rule Removing pbc first time ++++ 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: 648 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: 0.00e+00 Initial temperature: 310.917 K Started mdrun on rank 0 Thu Nov 19 22:43:01 2020 Step Time 0 0.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.16309e+03 -1.22598e+04 6.01457e+01 -1.00366e+04 1.68052e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.35608e+03 -8.35608e+03 3.12638e+02 1.39928e+03 Step Time 1000 2.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.86928e+03 -1.20548e+04 6.38866e+01 -1.01216e+04 1.60424e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.51737e+03 -8.35741e+03 2.98446e+02 -1.21277e+03 Step Time 2000 4.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.02578e+03 -1.21391e+04 7.28148e+01 -1.00405e+04 1.62285e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.41762e+03 -8.35723e+03 3.01908e+02 1.53102e+02 Step Time 3000 6.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.87716e+03 -1.18265e+04 7.00230e+01 -9.87931e+03 1.54840e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.33091e+03 -8.35516e+03 2.88058e+02 -4.09678e+02 Step Time 4000 8.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.98841e+03 -1.20337e+04 7.71543e+01 -9.96812e+03 1.62935e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.33878e+03 -8.35492e+03 3.03118e+02 1.29549e+02 Step Time 5000 10.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.04695e+03 -1.20562e+04 7.59592e+01 -9.93328e+03 1.58605e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.34722e+03 -8.35613e+03 2.95063e+02 5.40591e+02 Step Time 6000 12.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.11221e+03 -1.22123e+04 7.38102e+01 -1.00262e+04 1.56296e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.46329e+03 -8.35547e+03 2.90767e+02 6.59129e+02 Step Time 7000 14.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.91329e+03 -1.20132e+04 6.95727e+01 -1.00303e+04 1.66404e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.36625e+03 -8.35607e+03 3.09572e+02 -8.90185e+02 Step Time 8000 16.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.05926e+03 -1.19742e+04 7.48638e+01 -9.84010e+03 1.53705e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.30305e+03 -8.35403e+03 2.85947e+02 1.12590e+03 Step Time 9000 18.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.95584e+03 -1.19334e+04 6.82936e+01 -9.90928e+03 1.65471e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.25458e+03 -8.35340e+03 3.07835e+02 1.12609e+02 Step Time 10000 20.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.01477e+03 -1.18561e+04 7.81904e+01 -9.76318e+03 1.66309e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.10009e+03 -8.35369e+03 3.09395e+02 1.30549e+03 Step Time 11000 22.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.13496e+03 -1.22555e+04 8.40428e+01 -1.00364e+04 1.56493e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.47152e+03 -8.35249e+03 2.91133e+02 9.42768e+02 Step Time 12000 24.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.99552e+03 -1.20449e+04 7.13183e+01 -9.97808e+03 1.48815e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.48993e+03 -8.35478e+03 2.76850e+02 3.60492e+01 Step Time 13000 26.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.95985e+03 -1.19704e+04 6.36109e+01 -9.94695e+03 1.63946e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.30750e+03 -8.35475e+03 3.04998e+02 5.79845e+01 Step Time 14000 28.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.18800e+03 -1.22092e+04 8.85708e+01 -9.93265e+03 1.62483e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.30782e+03 -8.35559e+03 3.02277e+02 1.79483e+03 Step Time 15000 30.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.14300e+03 -1.20902e+04 7.83459e+01 -9.86883e+03 1.71294e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.15589e+03 -8.35534e+03 3.18669e+02 1.93191e+03 Step Time 16000 32.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.91421e+03 -1.17725e+04 8.13734e+01 -9.77695e+03 1.61639e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.16057e+03 -8.35461e+03 3.00706e+02 4.65776e+01 Step Time 17000 34.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.96920e+03 -1.21128e+04 8.11873e+01 -1.00624e+04 1.63711e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.42533e+03 -8.35652e+03 3.04561e+02 -3.36184e+02 Step Time 18000 36.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.03224e+03 -1.19940e+04 8.40468e+01 -9.87769e+03 1.54055e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.33714e+03 -8.35570e+03 2.86597e+02 8.06063e+02 Step Time 19000 38.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.81512e+03 -1.17703e+04 7.72935e+01 -9.87790e+03 1.50840e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.36950e+03 -8.35645e+03 2.80616e+02 -1.12453e+03 Step Time 20000 40.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.86970e+03 -1.18771e+04 8.19940e+01 -9.92535e+03 1.46590e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.45945e+03 -8.35480e+03 2.72711e+02 -7.21302e+02 Step Time 21000 42.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.08976e+03 -1.22170e+04 5.97183e+01 -1.00675e+04 1.63097e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.43655e+03 -8.35522e+03 3.03419e+02 8.11849e+02 Step Time 22000 44.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.23849e+03 -1.23599e+04 7.07320e+01 -1.00507e+04 1.60640e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.44428e+03 -8.35600e+03 2.98848e+02 1.97590e+03 Step Time 23000 46.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.94120e+03 -1.20171e+04 7.19560e+01 -1.00040e+04 1.59974e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.40422e+03 -8.35635e+03 2.97609e+02 -3.03241e+02 Step Time 24000 48.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.20485e+03 -1.24424e+04 6.15660e+01 -1.01760e+04 1.48843e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.68754e+03 -8.35563e+03 2.76901e+02 8.99296e+02 Step Time 25000 50.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.92897e+03 -1.20507e+04 7.38413e+01 -1.00479e+04 1.60361e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.44430e+03 -8.35569e+03 2.98329e+02 -6.51067e+02 Step Time 26000 52.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.11345e+03 -1.22429e+04 7.24308e+01 -1.00571e+04 1.63494e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.42213e+03 -8.35655e+03 3.04158e+02 8.80479e+02 Step Time 27000 54.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.93949e+03 -1.20017e+04 6.74084e+01 -9.99481e+03 1.64586e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.34895e+03 -8.35543e+03 3.06190e+02 -1.69471e+02 Step Time 28000 56.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.04691e+03 -1.21876e+04 7.69538e+01 -1.00638e+04 1.55859e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.50519e+03 -8.35460e+03 2.89954e+02 2.63484e+02 Step Time 29000 58.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.14597e+03 -1.22429e+04 7.03378e+01 -1.00266e+04 1.62251e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.40405e+03 -8.35518e+03 3.01846e+02 1.25001e+03 Step Time 30000 60.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.01920e+03 -1.22216e+04 6.75965e+01 -1.01348e+04 1.59491e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.53989e+03 -8.35436e+03 2.96710e+02 -3.13488e+02 Step Time 31000 62.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.02508e+03 -1.20020e+04 8.89659e+01 -9.88795e+03 1.65334e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.23461e+03 -8.35373e+03 3.07580e+02 6.13011e+02 Step Time 32000 64.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.15509e+03 -1.22502e+04 7.93269e+01 -1.00158e+04 1.62101e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.39476e+03 -8.35456e+03 3.01567e+02 1.38731e+03 Step Time 33000 66.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.09093e+03 -1.21422e+04 5.92195e+01 -9.99209e+03 1.60750e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.38460e+03 -8.35466e+03 2.99053e+02 8.79326e+02 Step Time 34000 68.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.06649e+03 -1.20341e+04 8.68381e+01 -9.88076e+03 1.63029e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.25047e+03 -8.35491e+03 3.03293e+02 1.13650e+03 Step Time 35000 70.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.79332e+03 -1.16145e+04 8.20916e+01 -9.73911e+03 1.50931e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.22980e+03 -8.35563e+03 2.80787e+02 -6.64004e+02 Step Time 36000 72.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.10112e+03 -1.20933e+04 7.98439e+01 -9.91230e+03 1.59267e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.31963e+03 -8.35562e+03 2.96294e+02 9.29741e+02 Step Time 37000 74.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.02173e+03 -1.20830e+04 6.35472e+01 -9.99768e+03 1.65541e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.34227e+03 -8.35706e+03 3.07966e+02 2.22337e+02 Step Time 38000 76.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.97579e+03 -1.19870e+04 7.65611e+01 -9.93463e+03 1.61486e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.31977e+03 -8.35747e+03 3.00422e+02 9.01528e+01 Step Time 39000 78.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.10866e+03 -1.22407e+04 7.91963e+01 -1.00528e+04 1.74149e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.31136e+03 -8.35598e+03 3.23980e+02 7.71328e+02 Step Time 40000 80.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.13013e+03 -1.23011e+04 7.32310e+01 -1.00977e+04 1.62005e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.47764e+03 -8.35593e+03 3.01387e+02 9.33178e+02 Step Time 41000 82.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.94146e+03 -1.20554e+04 8.22934e+01 -1.00317e+04 1.66286e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.36882e+03 -8.35462e+03 3.09353e+02 -3.01966e+02 Step Time 42000 84.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.09707e+03 -1.22457e+04 6.63230e+01 -1.00823e+04 1.58115e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.50117e+03 -8.35460e+03 2.94151e+02 6.25853e+02 Step Time 43000 86.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.03176e+03 -1.21798e+04 7.36457e+01 -1.00744e+04 1.54715e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.52728e+03 -8.35383e+03 2.87826e+02 -1.56469e+01 Step Time 44000 88.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.13398e+03 -1.24159e+04 7.07889e+01 -1.02111e+04 1.65283e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.55830e+03 -8.35475e+03 3.07486e+02 5.05231e+02 Step Time 45000 90.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.11146e+03 -1.22801e+04 6.38353e+01 -1.01048e+04 1.75430e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.35054e+03 -8.35623e+03 3.26362e+02 6.72490e+02 Step Time 46000 92.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.03957e+03 -1.20335e+04 6.95770e+01 -9.92433e+03 1.60287e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.32146e+03 -8.35571e+03 2.98192e+02 5.46079e+02 Step Time 47000 94.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.94641e+03 -1.20512e+04 6.76357e+01 -1.00371e+04 1.60190e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.43525e+03 -8.35567e+03 2.98011e+02 -2.82136e+02 Step Time 48000 96.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.89325e+03 -1.18672e+04 7.82336e+01 -9.89570e+03 1.74286e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.15283e+03 -8.35574e+03 3.24236e+02 -2.34121e+02 Step Time 49000 98.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.04773e+03 -1.19581e+04 6.59300e+01 -9.84442e+03 1.62782e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.21660e+03 -8.35430e+03 3.02834e+02 8.80224e+02 Step Time 50000 100.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.86235e+03 -1.18389e+04 7.80675e+01 -9.89848e+03 1.59263e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.30585e+03 -8.35530e+03 2.96287e+02 -6.19368e+02 Step Time 51000 102.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.03237e+03 -1.19831e+04 7.50980e+01 -9.87564e+03 1.63453e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.24111e+03 -8.35507e+03 3.04082e+02 7.07606e+02 Step Time 52000 104.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.12718e+03 -1.21948e+04 6.58533e+01 -1.00018e+04 1.66203e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.33974e+03 -8.35390e+03 3.09197e+02 1.31921e+03 Step Time 53000 106.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.32424e+03 -1.25177e+04 5.93573e+01 -1.01341e+04 1.59290e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.54117e+03 -8.35373e+03 2.96338e+02 2.38850e+03 Step Time 54000 108.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.01358e+03 -1.20306e+04 5.33235e+01 -9.96369e+03 1.62798e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.33571e+03 -8.35398e+03 3.02863e+02 6.18351e+02 Step Time 55000 110.00000 Writing checkpoint, step 55000 at Thu Nov 19 22:44:09 2020 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.18114e+03 -1.23373e+04 7.77983e+01 -1.00784e+04 1.63130e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.44708e+03 -8.35553e+03 3.03481e+02 1.45444e+03 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 55001 steps using 551 frames Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 2.02785e+03 -1.20844e+04 7.46624e+01 -9.98193e+03 1.61109e+03 Total Energy Conserved En. Temperature Pressure (bar) -8.37084e+03 -8.35533e+03 2.99720e+02 3.90752e+02 Total Virial (kJ/mol) 4.72585e+02 -5.02255e+00 -4.50474e+00 -5.02702e+00 4.54357e+02 -2.19077e+01 -4.49865e+00 -2.18893e+01 4.56256e+02 Pressure (bar) 3.28162e+02 2.82073e+01 2.49847e+01 2.82304e+01 4.33056e+02 1.14428e+02 2.49533e+01 1.14333e+02 4.11038e+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 832.917288 7496.256 1.5 NxN QSTab Elec. + LJ [F] 5493.967424 225252.664 45.7 NxN QSTab Elec. + LJ [V&F] 55.558368 3277.944 0.7 NxN QSTab Elec. [F] 5413.339408 184053.540 37.3 NxN QSTab Elec. [V&F] 54.758240 2245.088 0.5 Calc Weights 106.921944 3849.190 0.8 Spread Q Bspline 2281.001472 4562.003 0.9 Gather F Bspline 2281.001472 13686.009 2.8 3D-FFT 5406.818304 43254.546 8.8 Solve PME 14.080256 901.136 0.2 Shift-X 3.564648 21.388 0.0 Virial 0.381843 6.873 0.0 Stop-CM 0.357696 3.577 0.0 Calc-Ekin 7.129296 192.491 0.0 Constraint-V 35.641296 285.130 0.1 Constraint-Vir 0.357048 8.569 0.0 Settle 11.880648 3837.449 0.8 ----------------------------------------------------------------------------- Total 492933.854 100.0 ----------------------------------------------------------------------------- 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 Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Neighbor search 1 1 5501 7.280 18.158 10.7 Force 1 1 55001 46.299 115.488 68.2 PME mesh 1 1 55001 9.603 23.952 14.1 NB X/F buffer ops. 1 1 104501 0.384 0.959 0.6 Write traj. 1 1 1101 1.723 4.298 2.5 Update 1 1 55001 0.380 0.949 0.6 Constraints 1 1 55003 1.020 2.545 1.5 Rest 1.183 2.950 1.7 ----------------------------------------------------------------------------- Total 67.872 169.299 100.0 ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME spread 1 1 55001 3.073 7.665 4.5 PME gather 1 1 55001 3.682 9.183 5.4 PME 3D-FFT 1 1 110002 1.755 4.378 2.6 PME solve Elec 1 1 55001 0.967 2.413 1.4 ----------------------------------------------------------------------------- NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 67.870 67.872 100.0 (ns/day) (hour/ns) Performance: 140.032 0.171 Finished mdrun on rank 0 Thu Nov 19 22:44:09 2020