:-) GROMACS - gmx mdrun, 2021.3 (-: 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 2021.3 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan Process ID: 58606 Command line: gmx -quiet mdrun -deffnm nvep -ntmpi 1 -v true GROMACS version: 2021.3 Verified release checksum is c5bf577cc74de0e05106b7b6426476abb7f6530be7b4a2c64f637d6a6eca8fcb Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled 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/cc GNU 9.3.0 C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 9.3.0 C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG Running on 1 node with total 4 cores, 8 logical cores Hardware detected: CPU info: Vendor: Intel Brand: 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz Family: 6 Model: 140 Stepping: 1 Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Number of AVX-512 FMA units: 1 (AVX2 is faster w/o 2 AVX-512 FMA units) Hardware topology: Basic Sockets, cores, and logical processors: Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7] ++++ 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.5053201 -------- -------- --- Thank You --- -------- -------- The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1 Input Parameters: integrator = md tinit = 0 dt = 0.0005 nsteps = 10000 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -1646010373 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstcalcenergy = 100 nstenergy = 500 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 0.711399 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 0.711399 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 0.711399 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.16 fourier-nx = 12 fourier-ny = 12 fourier-nz = 12 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 tcoupl = No nsttcouple = -1 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p (3x3): ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = false qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = true 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: 1209 ref-t: 0 tau-t: 0 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 1 OpenMP thread NOTE: Thread affinity was not set. 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 0.227763 nm for Ewald Potential shift: LJ r^-12: -5.952e+01 r^-6: -7.715e+00, Ewald -1.406e-05 Initialized non-bonded Ewald tables, spacing: 7.87e-04 size: 905 Generated table with 855 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 855 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 855 data points for 1-4 LJ12. Tabscale = 500 points/nm Long Range LJ corr.: 4.1484e-04 Using SIMD 4x8 nonbonded short-range kernels Using a 4x8 pair-list setup: updated every 10 steps, buffer 0.000 nm, rlist 0.711 nm Using Lorentz-Berthelot Lennard-Jones combination rule There are: 404 Atoms 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 Thu Apr 28 23:06:12 2022 Step Time 0 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 5.99428e+01 3.56180e+02 1.08426e+02 6.24313e+01 -6.83991e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.66811e+03 -1.26387e+02 -1.88869e+02 -2.39119e+03 1.31181e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.66323e+03 1.12513e+03 -4.53810e+03 2.23858e+02 -7.58989e+02 Pressure (bar) 9.98538e+03 Step Time 500 0.25000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.25881e+02 2.33194e+02 7.37560e+01 5.42421e+01 -6.90217e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.67396e+03 -2.67822e+01 -1.88869e+02 -2.74424e+03 1.45849e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.80783e+03 1.26905e+03 -4.53878e+03 2.52492e+02 -7.58989e+02 Pressure (bar) -8.07414e+03 Step Time 1000 0.50000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.54823e+02 2.79331e+02 6.62055e+01 4.20885e+01 -6.77376e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.64784e+03 1.66437e+01 -1.88869e+02 -2.69774e+03 1.18650e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.76348e+03 1.22477e+03 -4.53871e+03 2.43683e+02 -7.58989e+02 Pressure (bar) 1.19652e+03 Step Time 1500 0.75000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.34694e+02 2.58759e+02 1.00357e+02 6.36489e+01 -6.95575e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.67504e+03 -8.12779e+01 -1.88869e+02 -2.59040e+03 1.27310e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.75777e+03 1.21899e+03 -4.53878e+03 2.42532e+02 -7.58989e+02 Pressure (bar) 7.92818e+02 Step Time 2000 1.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.96694e+02 3.11317e+02 7.99523e+01 6.08277e+01 -6.78185e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.66116e+03 -5.44866e+01 -1.88869e+02 -2.70159e+03 1.22550e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.74154e+03 1.20322e+03 -4.53832e+03 2.39395e+02 -7.58989e+02 Pressure (bar) -4.60449e+03 Step Time 2500 1.25000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.52754e+02 2.93479e+02 8.33528e+01 6.02577e+01 -6.93942e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.67242e+03 -4.20954e+01 -1.88869e+02 -2.68881e+03 1.27354e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.78193e+03 1.24283e+03 -4.53910e+03 2.47276e+02 -7.58989e+02 Pressure (bar) 5.62425e+02 Step Time 3000 1.50000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.97143e+02 2.69501e+02 8.74233e+01 6.83455e+01 -7.12990e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.69489e+03 7.64003e+01 -1.88869e+02 -2.84679e+03 1.25492e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.81337e+03 1.27466e+03 -4.53871e+03 2.53608e+02 -7.58989e+02 Pressure (bar) 9.92100e+02 Step Time 3500 1.75000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.89762e+02 2.85771e+02 8.38730e+01 5.10484e+01 -6.79658e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.65433e+03 2.62536e+01 -1.88869e+02 -2.77233e+03 1.29480e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.75614e+03 1.21805e+03 -4.53809e+03 2.42345e+02 -7.58989e+02 Pressure (bar) 2.45534e+02 Step Time 4000 2.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.54975e+02 3.18450e+02 7.77050e+01 5.47855e+01 -6.72105e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.64533e+03 -9.41769e+01 -1.88869e+02 -2.61913e+03 1.42950e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.70537e+03 1.16719e+03 -4.53818e+03 2.32225e+02 -7.58989e+02 Pressure (bar) -3.35894e+03 Step Time 4500 2.25000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.33481e+02 3.04330e+02 6.62906e+01 4.86214e+01 -7.00843e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.68251e+03 2.42634e+00 -1.88869e+02 -2.80236e+03 1.24136e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.80146e+03 1.26328e+03 -4.53819e+03 2.51343e+02 -7.58989e+02 Pressure (bar) 2.14624e+02 Step Time 5000 2.50000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.39930e+02 2.92891e+02 6.96768e+01 4.67481e+01 -6.73381e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.64604e+03 1.34066e+01 -1.88869e+02 -2.77588e+03 1.32168e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.72271e+03 1.18527e+03 -4.53744e+03 2.35823e+02 -7.58989e+02 Pressure (bar) -4.56350e+03 Step Time 5500 2.75000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.52495e+02 2.35887e+02 8.33571e+01 5.38983e+01 -6.82821e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.67800e+03 -4.82545e+01 -1.88869e+02 -2.61424e+03 1.47474e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.76308e+03 1.22459e+03 -4.53849e+03 2.43646e+02 -7.58989e+02 Pressure (bar) -1.02638e+03 Step Time 6000 3.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.13147e+02 2.39011e+02 7.33941e+01 5.34968e+01 -6.90967e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.66805e+03 -2.18502e+01 -1.88869e+02 -2.66729e+03 1.24804e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.74912e+03 1.21058e+03 -4.53853e+03 2.40860e+02 -7.58989e+02 Pressure (bar) 1.27520e+02 Step Time 6500 3.25000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.09016e+02 2.67246e+02 7.87046e+01 4.63376e+01 -6.84008e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.65858e+03 -2.66303e+01 -1.88869e+02 -2.75379e+03 1.41538e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.79187e+03 1.25337e+03 -4.53850e+03 2.49372e+02 -7.58989e+02 Pressure (bar) -7.49130e+02 Step Time 7000 3.50000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.09334e+02 2.45946e+02 7.02546e+01 4.56670e+01 -6.84456e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.65914e+03 2.07605e+01 -1.88869e+02 -2.71921e+03 1.12711e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.76939e+03 1.23114e+03 -4.53825e+03 2.44950e+02 -7.58989e+02 Pressure (bar) 1.46120e+03 Step Time 7500 3.75000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.49179e+02 2.52384e+02 9.55043e+01 7.34459e+01 -6.93976e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.68927e+03 -1.31437e+01 -1.88869e+02 -2.71160e+03 1.24890e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.71442e+03 1.17642e+03 -4.53800e+03 2.34063e+02 -7.58989e+02 Pressure (bar) -1.39160e+03 Step Time 8000 4.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.01540e+02 2.89778e+02 7.96111e+01 5.42763e+01 -6.87444e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.67127e+03 2.74904e+01 -1.88869e+02 -2.70070e+03 1.34246e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.68078e+03 1.14344e+03 -4.53733e+03 2.27501e+02 -7.58989e+02 Pressure (bar) 1.73129e+03 Step Time 8500 4.25000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.89698e+02 2.90379e+02 7.49347e+01 5.73303e+01 -6.88700e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.66852e+03 -7.42266e+01 -1.88869e+02 -2.63272e+03 1.30490e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.72838e+03 1.19016e+03 -4.53823e+03 2.36795e+02 -7.58989e+02 Pressure (bar) 6.72412e+02 Step Time 9000 4.50000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.07260e+02 2.93818e+02 7.52461e+01 4.52379e+01 -6.95643e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.68113e+03 -1.77533e+01 -1.88869e+02 -2.69938e+03 1.30683e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.74184e+03 1.20329e+03 -4.53855e+03 2.39408e+02 -7.58989e+02 Pressure (bar) -9.66020e+02 Step Time 9500 4.75000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.28822e+02 2.95144e+02 9.61802e+01 6.31835e+01 -6.87580e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.66657e+03 6.08919e+00 -1.88869e+02 -2.85020e+03 1.23600e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.79949e+03 1.26174e+03 -4.53775e+03 2.51039e+02 -7.58989e+02 Pressure (bar) 1.07906e+03 Step Time 10000 5.00000 Writing checkpoint, step 10000 at Thu Apr 28 23:06:14 2022 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 3.43095e+02 3.02972e+02 8.56095e+01 5.28222e+01 -6.79941e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.64613e+03 4.37440e+01 -1.88869e+02 -2.85200e+03 1.21920e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.74364e+03 1.20669e+03 -4.53695e+03 2.40084e+02 -7.58989e+02 Pressure (bar) -2.16015e+03 Energy conservation over simulation part #1 of length 5 ns, time 0 to 5 ns Conserved energy drift: 5.67e-04 kJ/mol/ps per atom <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 10001 steps using 101 frames Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 2.92533e+02 2.81408e+02 8.22884e+01 5.44070e+01 -6.86595e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -3.66662e+03 -1.00313e+01 -1.88869e+02 -2.72729e+03 1.31145e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -5.75789e+03 1.21962e+03 -4.53827e+03 2.42658e+02 -7.58989e+02 Pressure (bar) -7.07579e+02 Total Virial (kJ/mol) 4.81421e+02 -5.11129e+00 -4.31531e+00 -5.11134e+00 5.01042e+02 2.15936e+01 -4.31542e+00 2.15934e+01 5.02170e+02 Pressure (bar) -6.17553e+02 1.73841e+01 4.89267e+01 1.73845e+01 -7.36802e+02 -1.94815e+02 4.89275e+01 -1.94814e+02 -7.68383e+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 86.774298 780.969 1.2 NxN Ewald Elec. + LJ [F] 554.883184 36622.290 57.1 NxN Ewald Elec. + LJ [V&F] 5.670848 606.781 0.9 NxN Ewald Elec. [F] 316.401424 19300.487 30.1 NxN Ewald Elec. [V&F] 3.224800 270.883 0.4 1,4 nonbonded interactions 1.040104 93.609 0.1 Calc Weights 12.121212 436.364 0.7 Spread Q Bspline 258.585856 517.172 0.8 Gather F Bspline 258.585856 1551.515 2.4 3D-FFT 371.717168 2973.737 4.6 Solve PME 1.440144 92.169 0.1 Shift-X 0.404404 2.426 0.0 Bonds 2.910291 171.707 0.3 Angles 2.170217 364.596 0.6 Propers 1.040104 238.184 0.4 Impropers 0.390039 81.128 0.1 Virial 0.045349 0.816 0.0 Stop-CM 0.040804 0.408 0.0 Calc-Ekin 0.808808 21.838 0.0 ----------------------------------------------------------------------------- Total 64127.080 100.0 ----------------------------------------------------------------------------- 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 1001 0.355 0.996 17.4 Force 1 1 10001 1.211 3.396 59.2 PME mesh 1 1 10001 0.411 1.151 20.1 NB X/F buffer ops. 1 1 19001 0.017 0.049 0.9 Write traj. 1 1 21 0.023 0.064 1.1 Update 1 1 10001 0.012 0.033 0.6 Rest 0.016 0.044 0.8 ----------------------------------------------------------------------------- Total 2.045 5.733 100.0 ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME spread 1 1 10001 0.176 0.492 8.6 PME gather 1 1 10001 0.129 0.363 6.3 PME 3D-FFT 1 1 20002 0.051 0.143 2.5 PME solve Elec 1 1 10001 0.052 0.145 2.5 ----------------------------------------------------------------------------- NOTE: 17 % 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: 2.045 2.045 100.0 (ns/day) (hour/ns) Performance: 211.244 0.114 Finished mdrun on rank 0 Thu Apr 28 23:06:14 2022