:-) GROMACS - gmx mdrun, 2020.6-Debian-2020.6-2 (-: 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 2020.6-Debian-2020.6-2 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/student/adit/CMMDE_launching/larutan/SistemLarutan Process ID: 2570744 Command line: gmx -quiet mdrun -deffnm nvep -ntmpi 1 -v true GROMACS version: 2020.6-Debian-2020.6-2 Precision: single 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: disabled TNG support: enabled Hwloc support: hwloc-2.4.1 Tracing support: disabled C compiler: /usr/bin/cc GNU 10.2.1 C compiler flags: -msse4.1 -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 10.2.1 C++ compiler flags: -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG Running on 1 node with total 1 cores, 2 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU @ 2.20GHz Family: 6 Model: 79 Stepping: 0 Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 x2apic Hardware topology: Full, with devices Sockets, cores, and logical processors: Socket 0: [ 0 1] Numa nodes: Node 0 (8343068672 bytes mem): 0 1 Latency: 0 0 1.00 Caches: L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 2 ways L3: 57671680 bytes, linesize 64 bytes, assoc. 20, shared 2 ways PCI devices: 0000:00:04.0 Id: 1af4:1000 Class: 0x0200 Numa: 0 Highest SIMD level requested 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. 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 --- -------- -------- 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 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -140560403 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 = 0.961399 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 0.961399 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 0.961399 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.16 fourier-nx = 14 fourier-ny = 14 fourier-nz = 14 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 QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 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 grpopts: nrdf: 1293 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 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 0.307804 nm for Ewald Potential shift: LJ r^-12: -1.604e+00 r^-6: -1.266e+00, Ewald -1.040e-05 Initialized non-bonded Ewald tables, spacing: 9.15e-04 size: 1052 Generated table with 980 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 980 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 980 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SIMD 4x4 nonbonded short-range kernels Using a 4x4 pair-list setup: updated every 10 steps, buffer 0.000 nm, rlist 0.961 nm Using Lorentz-Berthelot Lennard-Jones combination rule Long Range LJ corr.: 3.6868e-04 There are: 432 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 Tue Jun 7 16:54:20 2022 Step Time 0 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.68571e+01 2.06130e+02 3.50263e+01 4.98516e+01 -4.70008e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.50551e+03 -3.10729e+02 -3.31483e+01 3.11356e+02 6.78661e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.15700e+03 1.17316e+03 -9.83849e+02 2.18249e+02 -5.67052e+01 Pressure (bar) 7.97352e+02 Step Time 500 0.25000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 5.71829e+01 1.80092e+02 3.09587e+01 5.62519e+01 -4.70784e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.50986e+03 -2.95917e+02 -3.31483e+01 2.92289e+02 7.71216e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.14974e+03 1.16607e+03 -9.83664e+02 2.16932e+02 -5.67052e+01 Pressure (bar) 2.98072e+02 Step Time 1000 0.50000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 6.69650e+01 2.01878e+02 3.47275e+01 5.17517e+01 -4.74050e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.51733e+03 -3.14749e+02 -3.31483e+01 2.74665e+02 7.15622e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.16842e+03 1.18507e+03 -9.83349e+02 2.20466e+02 -5.67052e+01 Pressure (bar) 4.11046e+01 Step Time 1500 0.75000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 5.89589e+01 2.01801e+02 2.84650e+01 4.74906e+01 -4.65939e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.50063e+03 -3.40624e+02 -3.31483e+01 2.76941e+02 8.30847e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.18232e+03 1.19856e+03 -9.83759e+02 2.22976e+02 -5.67052e+01 Pressure (bar) 5.79724e+02 Step Time 2000 1.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.35276e+01 1.92469e+02 3.61053e+01 5.95481e+01 -4.75944e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.53029e+03 -3.26461e+02 -3.31483e+01 2.72068e+02 7.07096e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.18023e+03 1.19672e+03 -9.83508e+02 2.22634e+02 -5.67052e+01 Pressure (bar) 4.29622e+02 Step Time 2500 1.25000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 7.04942e+01 1.88806e+02 4.12116e+01 6.39807e+01 -4.84451e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.53973e+03 -2.89260e+02 -3.31483e+01 2.52880e+02 6.06684e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.18894e+03 1.20491e+03 -9.84036e+02 2.24156e+02 -5.67052e+01 Pressure (bar) 7.94977e+02 Step Time 3000 1.50000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 6.47645e+01 1.71579e+02 2.34261e+01 5.25431e+01 -4.67042e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.50095e+03 -3.07265e+02 -3.31483e+01 2.95478e+02 7.64883e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.16176e+03 1.17794e+03 -9.83812e+02 2.19140e+02 -5.67052e+01 Pressure (bar) 5.99587e+02 Step Time 3500 1.75000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 9.43893e+01 1.61463e+02 2.44596e+01 6.38215e+01 -4.68754e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.50223e+03 -2.84392e+02 -3.31483e+01 2.26656e+02 6.90088e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.18466e+03 1.20142e+03 -9.83235e+02 2.23508e+02 -5.67052e+01 Pressure (bar) 3.79233e+02 Step Time 4000 2.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 9.04692e+01 1.52852e+02 2.61851e+01 4.55728e+01 -4.76396e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.52034e+03 -3.01335e+02 -3.31483e+01 2.98707e+02 7.06226e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.17518e+03 1.19173e+03 -9.83449e+02 2.21705e+02 -5.67052e+01 Pressure (bar) 9.28437e+02 Step Time 4500 2.25000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.07335e+01 1.79767e+02 4.54518e+01 5.96417e+01 -4.80120e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.52796e+03 -3.17002e+02 -3.31483e+01 3.03310e+02 7.60940e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.13792e+03 1.15426e+03 -9.83658e+02 2.14734e+02 -5.67052e+01 Pressure (bar) -3.71822e+02 Step Time 5000 2.50000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.83895e+01 1.35048e+02 4.58026e+01 7.27292e+01 -4.87079e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.52845e+03 -3.30437e+02 -3.31483e+01 2.83694e+02 7.64058e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.19483e+03 1.21136e+03 -9.83477e+02 2.25356e+02 -5.67052e+01 Pressure (bar) -4.40553e+02 Step Time 5500 2.75000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.33474e+01 1.60111e+02 2.49346e+01 4.50281e+01 -4.84969e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.52294e+03 -3.44011e+02 -3.31483e+01 2.92817e+02 7.44514e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.22426e+03 1.24060e+03 -9.83656e+02 2.30797e+02 -5.67052e+01 Pressure (bar) 1.18631e+03 Step Time 6000 3.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 6.61491e+01 1.99206e+02 2.83812e+01 4.32869e+01 -4.63137e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.50879e+03 -3.48650e+02 -3.31483e+01 3.06267e+02 7.48799e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.17705e+03 1.19348e+03 -9.83563e+02 2.22031e+02 -5.67052e+01 Pressure (bar) -3.32347e+02 Step Time 6500 3.25000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.83938e+01 1.59127e+02 4.40262e+01 6.20234e+01 -4.86572e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.52597e+03 -3.25515e+02 -3.31483e+01 2.94908e+02 7.41591e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.16686e+03 1.18353e+03 -9.83332e+02 2.20180e+02 -5.67052e+01 Pressure (bar) 4.52560e+02 Step Time 7000 3.50000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.94784e+01 1.77594e+02 2.43321e+01 3.49407e+01 -4.80416e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.52508e+03 -3.12532e+02 -3.31483e+01 2.73032e+02 6.57994e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.21039e+03 1.22704e+03 -9.83349e+02 2.28273e+02 -5.67052e+01 Pressure (bar) 8.73185e+02 Step Time 7500 3.75000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 9.28125e+01 1.62232e+02 3.35552e+01 5.94787e+01 -4.71466e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.51767e+03 -2.95079e+02 -3.31483e+01 2.72958e+02 7.00983e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.15948e+03 1.17609e+03 -9.83393e+02 2.18795e+02 -5.67052e+01 Pressure (bar) -5.48705e+02 Step Time 8000 4.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 9.96638e+01 1.62056e+02 2.80954e+01 5.80195e+01 -4.63848e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.49588e+03 -3.25313e+02 -3.31483e+01 2.86824e+02 7.14535e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.15287e+03 1.16952e+03 -9.83342e+02 2.17574e+02 -5.67052e+01 Pressure (bar) 2.97416e+02 Step Time 8500 4.25000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 9.72742e+01 1.36549e+02 4.99397e+01 7.40676e+01 -4.85137e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.54643e+03 -2.83260e+02 -3.31483e+01 3.23393e+02 6.66151e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.11986e+03 1.13679e+03 -9.83069e+02 2.11484e+02 -5.67052e+01 Pressure (bar) 9.45151e+02 Step Time 9000 4.50000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.24089e+01 1.79101e+02 3.29559e+01 4.82325e+01 -4.74104e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.51091e+03 -2.87232e+02 -3.31483e+01 2.83039e+02 6.98197e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.14047e+03 1.15701e+03 -9.83462e+02 2.15245e+02 -5.67052e+01 Pressure (bar) 5.52506e+02 Step Time 9500 4.75000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.46766e+01 1.58841e+02 4.20994e+01 6.14774e+01 -4.84161e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.52382e+03 -2.96920e+02 -3.31483e+01 2.45470e+02 6.73681e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.19880e+03 1.21528e+03 -9.83517e+02 2.26086e+02 -5.67052e+01 Pressure (bar) -5.11383e+02 Step Time 10000 5.00000 Writing checkpoint, step 10000 at Tue Jun 7 16:54:27 2022 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.67398e+01 1.65914e+02 5.29682e+01 6.75271e+01 -4.83456e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.53760e+03 -3.09650e+02 -3.31483e+01 3.06939e+02 6.95346e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.13561e+03 1.15236e+03 -9.83256e+02 2.14380e+02 -5.67052e+01 Pressure (bar) 4.15713e+02 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 10001 steps using 101 frames Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.47749e+01 1.65731e+02 3.59536e+01 5.62230e+01 -4.76393e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.51942e+03 -3.09137e+02 -3.31483e+01 2.87991e+02 7.15408e+01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -2.16426e+03 1.18071e+03 -9.83545e+02 2.19655e+02 -5.67052e+01 Pressure (bar) 3.09581e+02 Total Virial (kJ/mol) 2.92701e+02 2.08917e+01 -3.05352e+00 2.08916e+01 3.00999e+02 4.96721e-02 -3.05346e+00 4.97567e-02 3.14731e+02 Pressure (bar) 3.54393e+02 -9.94881e+01 1.26737e+01 -9.94881e+01 3.11738e+02 -1.17409e+01 1.26735e+01 -1.17412e+01 2.62611e+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 69.718542 627.467 1.5 NxN QSTab Elec. + LJ [F] 519.912272 21316.403 52.3 NxN QSTab Elec. + LJ [V&F] 5.310760 313.335 0.8 NxN QSTab Elec. [F] 283.296912 9632.095 23.7 NxN QSTab Elec. [V&F] 2.910824 119.344 0.3 1,4 nonbonded interactions 0.720072 64.806 0.2 Calc Weights 12.961296 466.607 1.1 Spread Q Bspline 276.507648 553.015 1.4 Gather F Bspline 276.507648 1659.046 4.1 3D-FFT 626.902684 5015.221 12.3 Solve PME 1.960196 125.453 0.3 Shift-X 0.432432 2.595 0.0 Bonds 3.080308 181.738 0.4 Angles 2.260226 379.718 0.9 Propers 0.270027 61.836 0.2 RB-Dihedrals 0.720072 177.858 0.4 Virial 0.048177 0.867 0.0 Stop-CM 0.043632 0.436 0.0 Calc-Ekin 0.864864 23.351 0.1 ----------------------------------------------------------------------------- Total 40721.192 100.0 ----------------------------------------------------------------------------- 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 0.836 1.840 11.0 Force 1 1 10001 4.878 10.732 64.4 PME mesh 1 1 10001 1.647 3.623 21.7 NB X/F buffer ops. 1 1 19001 0.061 0.133 0.8 Write traj. 1 1 21 0.022 0.048 0.3 Update 1 1 10001 0.045 0.099 0.6 Rest 0.089 0.195 1.2 ----------------------------------------------------------------------------- Total 7.577 16.670 100.0 ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME spread 1 1 10001 0.469 1.031 6.2 PME gather 1 1 10001 0.676 1.486 8.9 PME 3D-FFT 1 1 20002 0.296 0.651 3.9 PME solve Elec 1 1 10001 0.194 0.428 2.6 ----------------------------------------------------------------------------- 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: 7.577 7.577 100.0 (ns/day) (hour/ns) Performance: 57.020 0.421 Finished mdrun on rank 0 Tue Jun 7 16:54:27 2022