:-) 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: 2570737 Command line: gmx -quiet mdrun -deffnm nvt -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 = 0.001 nsteps = 1000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 2101298815 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 100 nstvout = 0 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 = 0.961399 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 = 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: 1012 ref-t: 298.15 tau-t: 0.1 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Changing nstlist from 10 to 100, rlist from 0.961399 to 0.961399 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 100 steps, buffer 0.000 nm, rlist 0.961 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: updated every 100 steps, buffer 0.119 nm, rlist 1.080 nm Using Lorentz-Berthelot Lennard-Jones combination rule Long Range LJ corr.: 3.6868e-04 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 281 ++++ 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: 432 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: 6.46e-07 Initial temperature: 303.569 K Started mdrun on rank 0 Tue Jun 7 16:54:18 2022 Step Time 0 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 7.53202e+00 3.22554e+01 2.42243e+01 2.97818e+01 -4.76251e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.50927e+03 -4.22464e+02 -3.37410e+01 -1.66597e+01 3.19699e+01 Potential Kinetic En. Total Energy Conserved En. Temperature -2.86113e+03 1.27811e+03 -1.58303e+03 -1.58303e+03 3.03797e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -5.87450e+01 -3.42106e+01 6.57980e-07 Step Time 1000 1.00000 Writing checkpoint, step 1000 at Tue Jun 7 16:54:18 2022 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 3.51747e+01 1.84321e+02 3.77233e+01 7.31505e+01 -4.79605e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.52513e+03 -3.16425e+02 -3.37410e+01 2.95999e+02 7.23590e+01 Potential Kinetic En. Total Energy Conserved En. Temperature -2.18136e+03 1.20932e+03 -9.72044e+02 -1.57863e+03 2.87446e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -5.87450e+01 5.07352e+02 7.49168e-07 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 1001 steps using 11 frames Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.26678e+01 1.50638e+02 3.84769e+01 5.46640e+01 -4.77874e+00 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -2.52157e+03 -3.37459e+02 -3.37410e+01 2.26510e+02 6.15578e+01 Potential Kinetic En. Total Energy Conserved En. Temperature -2.34303e+03 1.25062e+03 -1.09241e+03 -1.57934e+03 2.97264e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -5.87450e+01 4.33180e+02 0.00000e+00 Total Virial (kJ/mol) 2.27897e+02 -2.39683e+01 -4.34334e+01 -2.39683e+01 3.04155e+02 3.35767e+01 -4.34333e+01 3.35766e+01 3.44256e+02 Pressure (bar) 6.59207e+02 1.12818e+02 1.55373e+02 1.12819e+02 3.63445e+02 -1.56211e+02 1.55372e+02 -1.56210e+02 2.76890e+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 0.748886 6.740 0.2 NxN QSTab Elec. + LJ [F] 52.605432 2156.823 53.2 NxN QSTab Elec. + LJ [V&F] 0.585672 34.555 0.9 NxN QSTab Elec. [F] 28.093032 955.163 23.6 NxN QSTab Elec. [V&F] 0.312632 12.818 0.3 1,4 nonbonded interactions 0.072072 6.486 0.2 Calc Weights 1.297296 46.703 1.2 Spread Q Bspline 27.675648 55.351 1.4 Gather F Bspline 27.675648 166.054 4.1 3D-FFT 62.746684 501.973 12.4 Solve PME 0.196196 12.557 0.3 Shift-X 0.004752 0.029 0.0 Bonds 0.027027 1.595 0.0 Angles 0.226226 38.006 0.9 Propers 0.027027 6.189 0.2 RB-Dihedrals 0.072072 17.802 0.4 Virial 0.005247 0.094 0.0 Stop-CM 0.005184 0.052 0.0 Calc-Ekin 0.087264 2.356 0.1 Lincs 0.281843 16.911 0.4 Lincs-Mat 1.961868 7.847 0.2 Constraint-V 0.563124 4.505 0.1 Constraint-Vir 0.003091 0.074 0.0 ----------------------------------------------------------------------------- Total 4050.682 100.0 ----------------------------------------------------------------------------- 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 11 0.009 0.019 1.4 Force 1 1 1001 0.400 0.881 65.8 PME mesh 1 1 1001 0.136 0.299 22.4 NB X/F buffer ops. 1 1 1991 0.005 0.011 0.8 Write traj. 1 1 11 0.025 0.056 4.2 Update 1 1 1001 0.004 0.009 0.7 Constraints 1 1 1003 0.023 0.050 3.7 Rest 0.006 0.013 1.0 ----------------------------------------------------------------------------- Total 0.609 1.339 100.0 ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME spread 1 1 1001 0.040 0.088 6.6 PME gather 1 1 1001 0.055 0.122 9.1 PME 3D-FFT 1 1 2002 0.024 0.053 3.9 PME solve Elec 1 1 1001 0.016 0.035 2.6 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 0.608 0.609 100.0 (ns/day) (hour/ns) Performance: 142.115 0.169 Finished mdrun on rank 0 Tue Jun 7 16:54:18 2022