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615 lines
26 KiB
615 lines
26 KiB
:-) GROMACS - gmx mdrun, 2020.6-Debian-2020.6-2 (-: |
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GROMACS is written by: |
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Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen |
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Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd |
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Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray |
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Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang |
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Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis |
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Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson |
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Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund |
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Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall |
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Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov |
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Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen |
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Christian Wennberg Maarten Wolf Artem Zhmurov |
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and the project leaders: |
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Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel |
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Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
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Copyright (c) 2001-2019, The GROMACS development team at |
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Uppsala University, Stockholm University and |
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the Royal Institute of Technology, Sweden. |
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check out http://www.gromacs.org for more information. |
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GROMACS is free software; you can redistribute it and/or modify it |
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under the terms of the GNU Lesser General Public License |
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as published by the Free Software Foundation; either version 2.1 |
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of the License, or (at your option) any later version. |
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GROMACS: gmx mdrun, version 2020.6-Debian-2020.6-2 |
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Executable: /usr/bin/gmx |
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Data prefix: /usr |
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Working dir: /home/student/adit/CMMDE_launching/larutan/SistemLarutan |
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Process ID: 2570733 |
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Command line: |
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gmx -quiet mdrun -deffnm nve -ntmpi 1 -v true |
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GROMACS version: 2020.6-Debian-2020.6-2 |
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Precision: single |
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Memory model: 64 bit |
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MPI library: thread_mpi |
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OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) |
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GPU support: disabled |
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SIMD instructions: SSE4.1 |
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FFT library: fftw-3.3.8-sse2-avx |
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RDTSCP usage: disabled |
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TNG support: enabled |
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Hwloc support: hwloc-2.4.1 |
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Tracing support: disabled |
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C compiler: /usr/bin/cc GNU 10.2.1 |
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C compiler flags: -msse4.1 -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG |
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C++ compiler: /usr/bin/c++ GNU 10.2.1 |
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C++ compiler flags: -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG |
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Running on 1 node with total 1 cores, 2 logical cores |
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Hardware detected: |
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CPU info: |
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Vendor: Intel |
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Brand: Intel(R) Xeon(R) CPU @ 2.20GHz |
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Family: 6 Model: 79 Stepping: 0 |
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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 |
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Hardware topology: Full, with devices |
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Sockets, cores, and logical processors: |
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Socket 0: [ 0 1] |
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Numa nodes: |
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Node 0 (8343068672 bytes mem): 0 1 |
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Latency: |
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0 |
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0 1.00 |
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Caches: |
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L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways |
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L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 2 ways |
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L3: 57671680 bytes, linesize 64 bytes, assoc. 20, shared 2 ways |
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PCI devices: |
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0000:00:04.0 Id: 1af4:1000 Class: 0x0200 Numa: 0 |
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Highest SIMD level requested by all nodes in run: AVX2_256 |
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SIMD instructions selected at compile time: SSE4.1 |
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This program was compiled for different hardware than you are running on, |
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which could influence performance. |
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The current CPU can measure timings more accurately than the code in |
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gmx mdrun was configured to use. This might affect your simulation |
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speed as accurate timings are needed for load-balancing. |
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Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. |
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|
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. |
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Lindahl |
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GROMACS: High performance molecular simulations through multi-level |
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parallelism from laptops to supercomputers |
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SoftwareX 1 (2015) pp. 19-25 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl |
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with |
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GROMACS |
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. |
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl |
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GROMACS 4.5: a high-throughput and highly parallel open source molecular |
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simulation toolkit |
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Bioinformatics 29 (2013) pp. 845-54 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl |
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable |
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molecular simulation |
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J. Chem. Theory Comput. 4 (2008) pp. 435-447 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. |
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Berendsen |
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GROMACS: Fast, Flexible and Free |
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J. Comp. Chem. 26 (2005) pp. 1701-1719 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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E. Lindahl and B. Hess and D. van der Spoel |
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GROMACS 3.0: A package for molecular simulation and trajectory analysis |
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J. Mol. Mod. 7 (2001) pp. 306-317 |
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-------- -------- --- Thank You --- -------- -------- |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen |
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GROMACS: A message-passing parallel molecular dynamics implementation |
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Comp. Phys. Comm. 91 (1995) pp. 43-56 |
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-------- -------- --- Thank You --- -------- -------- |
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The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1 |
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Input Parameters: |
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integrator = md |
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tinit = 0 |
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dt = 0.001 |
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nsteps = 1000 |
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init-step = 0 |
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simulation-part = 1 |
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comm-mode = Linear |
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nstcomm = 100 |
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bd-fric = 0 |
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ld-seed = -1444938113 |
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emtol = 10 |
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emstep = 0.01 |
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niter = 20 |
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fcstep = 0 |
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nstcgsteep = 1000 |
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nbfgscorr = 10 |
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rtpi = 0.05 |
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nstxout = 100 |
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nstvout = 0 |
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nstfout = 0 |
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nstlog = 100 |
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nstcalcenergy = 100 |
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nstenergy = 100 |
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nstxout-compressed = 0 |
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compressed-x-precision = 1000 |
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cutoff-scheme = Verlet |
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nstlist = 10 |
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pbc = xyz |
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periodic-molecules = false |
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verlet-buffer-tolerance = -1 |
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rlist = 1.05754 |
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coulombtype = PME |
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coulomb-modifier = Potential-shift |
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rcoulomb-switch = 0 |
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rcoulomb = 0.961399 |
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epsilon-r = 1 |
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epsilon-rf = inf |
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vdw-type = Cut-off |
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vdw-modifier = Potential-shift |
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rvdw-switch = 0 |
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rvdw = 0.961399 |
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DispCorr = EnerPres |
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table-extension = 1 |
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fourierspacing = 0.16 |
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fourier-nx = 14 |
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fourier-ny = 14 |
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fourier-nz = 14 |
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pme-order = 4 |
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ewald-rtol = 1e-05 |
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ewald-rtol-lj = 0.001 |
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lj-pme-comb-rule = Geometric |
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ewald-geometry = 0 |
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epsilon-surface = 0 |
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tcoupl = No |
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nsttcouple = -1 |
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nh-chain-length = 0 |
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print-nose-hoover-chain-variables = false |
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pcoupl = No |
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pcoupltype = Isotropic |
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nstpcouple = -1 |
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tau-p = 1 |
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compressibility (3x3): |
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compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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ref-p (3x3): |
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ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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refcoord-scaling = No |
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posres-com (3): |
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posres-com[0]= 0.00000e+00 |
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posres-com[1]= 0.00000e+00 |
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posres-com[2]= 0.00000e+00 |
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posres-comB (3): |
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posres-comB[0]= 0.00000e+00 |
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posres-comB[1]= 0.00000e+00 |
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posres-comB[2]= 0.00000e+00 |
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QMMM = false |
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QMconstraints = 0 |
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QMMMscheme = 0 |
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MMChargeScaleFactor = 1 |
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qm-opts: |
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ngQM = 0 |
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constraint-algorithm = Lincs |
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continuation = false |
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Shake-SOR = false |
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shake-tol = 0.0001 |
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lincs-order = 4 |
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lincs-iter = 1 |
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lincs-warnangle = 30 |
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nwall = 0 |
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wall-type = 9-3 |
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wall-r-linpot = -1 |
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wall-atomtype[0] = -1 |
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wall-atomtype[1] = -1 |
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wall-density[0] = 0 |
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wall-density[1] = 0 |
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wall-ewald-zfac = 3 |
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pull = false |
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awh = false |
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rotation = false |
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interactiveMD = false |
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disre = No |
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disre-weighting = Conservative |
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disre-mixed = false |
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dr-fc = 1000 |
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dr-tau = 0 |
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nstdisreout = 100 |
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orire-fc = 0 |
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orire-tau = 0 |
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nstorireout = 100 |
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free-energy = no |
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cos-acceleration = 0 |
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deform (3x3): |
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deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} |
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simulated-tempering = false |
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swapcoords = no |
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userint1 = 0 |
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userint2 = 0 |
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userint3 = 0 |
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userint4 = 0 |
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userreal1 = 0 |
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userreal2 = 0 |
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userreal3 = 0 |
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userreal4 = 0 |
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applied-forces: |
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electric-field: |
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x: |
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E0 = 0 |
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omega = 0 |
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t0 = 0 |
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sigma = 0 |
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y: |
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E0 = 0 |
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omega = 0 |
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t0 = 0 |
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sigma = 0 |
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z: |
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E0 = 0 |
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omega = 0 |
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t0 = 0 |
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sigma = 0 |
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density-guided-simulation: |
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active = false |
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group = protein |
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similarity-measure = inner-product |
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atom-spreading-weight = unity |
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force-constant = 1e+09 |
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gaussian-transform-spreading-width = 0.2 |
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gaussian-transform-spreading-range-in-multiples-of-width = 4 |
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reference-density-filename = reference.mrc |
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nst = 1 |
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normalize-densities = true |
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adaptive-force-scaling = false |
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adaptive-force-scaling-time-constant = 4 |
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grpopts: |
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nrdf: 1012 |
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ref-t: 0 |
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tau-t: 0 |
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annealing: No |
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annealing-npoints: 0 |
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acc: 0 0 0 |
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nfreeze: N N N |
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energygrp-flags[ 0]: 0 |
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Can not increase nstlist because an NVE ensemble is used |
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Using 1 MPI thread |
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Non-default thread affinity set, disabling internal thread affinity |
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Using 1 OpenMP thread |
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System total charge: -0.000 |
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Will do PME sum in reciprocal space for electrostatic interactions. |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen |
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A smooth particle mesh Ewald method |
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J. Chem. Phys. 103 (1995) pp. 8577-8592 |
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-------- -------- --- Thank You --- -------- -------- |
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Using a Gaussian width (1/beta) of 0.307804 nm for Ewald |
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Potential shift: LJ r^-12: -1.604e+00 r^-6: -1.266e+00, Ewald -1.040e-05 |
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Initialized non-bonded Ewald tables, spacing: 9.15e-04 size: 1052 |
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Generated table with 1028 data points for 1-4 COUL. |
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Tabscale = 500 points/nm |
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Generated table with 1028 data points for 1-4 LJ6. |
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Tabscale = 500 points/nm |
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Generated table with 1028 data points for 1-4 LJ12. |
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Tabscale = 500 points/nm |
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Using SIMD 4x4 nonbonded short-range kernels |
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Using a 4x4 pair-list setup: |
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updated every 10 steps, buffer 0.096 nm, rlist 1.058 nm |
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Using Lorentz-Berthelot Lennard-Jones combination rule |
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Long Range LJ corr.: <C6> 3.6868e-04 |
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Removing pbc first time |
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Initializing LINear Constraint Solver |
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ |
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B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije |
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LINCS: A Linear Constraint Solver for molecular simulations |
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J. Comp. Chem. 18 (1997) pp. 1463-1472 |
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-------- -------- --- Thank You --- -------- -------- |
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The number of constraints is 281 |
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There are: 432 Atoms |
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Constraining the starting coordinates (step 0) |
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Constraining the coordinates at t0-dt (step 0) |
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Center of mass motion removal mode is Linear |
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We have the following groups for center of mass motion removal: |
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0: rest |
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RMS relative constraint deviation after constraining: 2.82e-07 |
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Initial temperature: 9.19637e-08 K |
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Started mdrun on rank 0 Tue Jun 7 16:54:17 2022 |
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Step Time |
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0 0.00000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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6.54106e+00 2.91333e+01 2.05991e+01 2.39229e+01 -4.72959e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.50213e+03 -3.84107e+02 -3.37410e+01 2.37485e+02 6.25183e+01 |
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Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
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-2.54450e+03 1.43772e-01 -2.54436e+03 3.41735e-02 -5.87450e+01 |
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Pressure (bar) Constr. rmsd |
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-1.02412e+03 3.10957e-07 |
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Step Time |
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100 0.10000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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6.06172e+00 2.53319e+01 2.26869e+01 2.81504e+01 -4.76577e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.50754e+03 -3.93727e+02 -3.37410e+01 1.09030e+02 3.58492e+01 |
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Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
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-2.71266e+03 1.68273e+02 -2.54439e+03 3.99971e+01 -5.87450e+01 |
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Pressure (bar) Constr. rmsd |
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-1.31114e+03 4.66734e-07 |
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Step Time |
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200 0.20000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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6.24788e+00 2.79298e+01 2.16709e+01 2.69609e+01 -4.75449e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.50610e+03 -3.69433e+02 -3.37410e+01 4.82246e+01 3.25844e+01 |
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Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
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-2.75041e+03 2.06001e+02 -2.54441e+03 4.89650e+01 -5.87450e+01 |
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Pressure (bar) Constr. rmsd |
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-8.55580e+02 4.46975e-07 |
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Step Time |
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300 0.30000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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7.03768e+00 3.23298e+01 1.93120e+01 2.62972e+01 -4.76136e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.50757e+03 -3.48475e+02 -3.37410e+01 -1.00443e+01 4.04671e+01 |
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Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
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-2.77915e+03 2.34761e+02 -2.54439e+03 5.58008e+01 -5.87450e+01 |
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Pressure (bar) Constr. rmsd |
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-4.48931e+02 5.61386e-07 |
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Step Time |
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400 0.40000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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6.35392e+00 3.06192e+01 2.04599e+01 2.71354e+01 -4.76162e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.50950e+03 -3.65008e+02 -3.37410e+01 -1.01754e+01 3.59214e+01 |
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Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
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-2.80269e+03 2.58293e+02 -2.54440e+03 6.13943e+01 -5.87450e+01 |
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Pressure (bar) Constr. rmsd |
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-4.52210e+02 5.29885e-07 |
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Step Time |
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500 0.50000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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6.71373e+00 3.63823e+01 1.92696e+01 2.34328e+01 -4.75007e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.50640e+03 -3.86323e+02 -3.37410e+01 -1.36942e+01 3.75627e+01 |
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Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
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-2.82155e+03 2.77155e+02 -2.54439e+03 6.58776e+01 -5.87450e+01 |
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Pressure (bar) Constr. rmsd |
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-4.94223e+02 5.68981e-07 |
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Step Time |
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600 0.60000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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7.17528e+00 3.61834e+01 1.94872e+01 2.38956e+01 -4.72431e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.50299e+03 -3.67483e+02 -3.37410e+01 -4.33854e+01 3.32332e+01 |
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Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
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-2.83235e+03 2.87970e+02 -2.54438e+03 6.84482e+01 -5.87450e+01 |
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Pressure (bar) Constr. rmsd |
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-2.13021e+02 5.15836e-07 |
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Step Time |
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700 0.70000 |
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Energies (kJ/mol) |
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
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7.22778e+00 2.50161e+01 2.74334e+01 3.88358e+01 -4.81276e+00 |
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
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-2.51810e+03 -3.79901e+02 -3.37410e+01 -3.59257e+01 3.84723e+01 |
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Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
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-2.83549e+03 2.91116e+02 -2.54438e+03 6.91960e+01 -5.87450e+01 |
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Pressure (bar) Constr. rmsd |
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-2.15106e+02 4.83708e-07 |
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Step Time |
|
800 0.80000 |
|
|
|
Energies (kJ/mol) |
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
|
6.43240e+00 3.41687e+01 2.00180e+01 2.57901e+01 -4.71745e+00 |
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
|
-2.50144e+03 -3.96256e+02 -3.37410e+01 -4.61304e+01 3.06076e+01 |
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
|
-2.86526e+03 3.20859e+02 -2.54441e+03 7.62656e+01 -5.87450e+01 |
|
Pressure (bar) Constr. rmsd |
|
-3.63740e+02 5.47719e-07 |
|
|
|
Step Time |
|
900 0.90000 |
|
|
|
Energies (kJ/mol) |
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
|
6.79160e+00 2.44255e+01 3.01078e+01 3.90440e+01 -4.82324e+00 |
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
|
-2.51791e+03 -3.95682e+02 -3.37410e+01 -1.92854e+01 3.18689e+01 |
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
|
-2.83921e+03 2.94802e+02 -2.54440e+03 7.00722e+01 -5.87450e+01 |
|
Pressure (bar) Constr. rmsd |
|
-3.28353e+02 5.09151e-07 |
|
|
|
Step Time |
|
1000 1.00000 |
|
|
|
Writing checkpoint, step 1000 at Tue Jun 7 16:54:17 2022 |
|
|
|
|
|
Energies (kJ/mol) |
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 |
|
5.75652e+00 3.03379e+01 2.45278e+01 2.99435e+01 -4.75696e+00 |
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
|
-2.50845e+03 -4.22441e+02 -3.37410e+01 -1.67431e+01 3.18578e+01 |
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
|
-2.86370e+03 3.19295e+02 -2.54441e+03 7.58940e+01 -5.87450e+01 |
|
Pressure (bar) Constr. rmsd |
|
-5.42659e+02 5.41240e-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 |
|
6.57633e+00 3.01689e+01 2.23248e+01 2.84917e+01 -4.75978e+00 |
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. |
|
-2.50801e+03 -3.82621e+02 -3.37410e+01 1.81233e+01 3.73585e+01 |
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar) |
|
-2.78609e+03 2.41697e+02 -2.54439e+03 5.74496e+01 -5.87450e+01 |
|
Pressure (bar) Constr. rmsd |
|
-5.68099e+02 0.00000e+00 |
|
|
|
Total Virial (kJ/mol) |
|
2.16868e+02 -2.86846e+00 -7.15539e+00 |
|
-2.86852e+00 2.46440e+02 1.69101e+00 |
|
-7.15540e+00 1.69097e+00 2.69289e+02 |
|
|
|
Pressure (bar) |
|
-4.83086e+02 8.99856e+00 3.20358e+01 |
|
8.99877e+00 -5.72498e+02 1.58591e-02 |
|
3.20358e+01 1.59669e-02 -6.48712e+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 7.419880 66.779 1.4 |
|
NxN QSTab Elec. + LJ [F] 65.248280 2675.179 54.5 |
|
NxN QSTab Elec. + LJ [V&F] 0.731792 43.176 0.9 |
|
NxN QSTab Elec. [F] 35.851224 1218.942 24.8 |
|
NxN QSTab Elec. [V&F] 0.399776 16.391 0.3 |
|
1,4 nonbonded interactions 0.072072 6.486 0.1 |
|
Calc Weights 1.297296 46.703 1.0 |
|
Spread Q Bspline 27.675648 55.351 1.1 |
|
Gather F Bspline 27.675648 166.054 3.4 |
|
3D-FFT 62.746684 501.973 10.2 |
|
Solve PME 0.196196 12.557 0.3 |
|
Shift-X 0.043632 0.262 0.0 |
|
Bonds 0.027027 1.595 0.0 |
|
Angles 0.226226 38.006 0.8 |
|
Propers 0.027027 6.189 0.1 |
|
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 0.0 |
|
Lincs 0.281843 16.911 0.3 |
|
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 4905.284 100.0 |
|
----------------------------------------------------------------------------- |
|
|
|
|
|
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 1 101 0.092 0.203 9.6 |
|
Force 1 1 1001 0.616 1.354 64.2 |
|
PME mesh 1 1 1001 0.171 0.375 17.8 |
|
NB X/F buffer ops. 1 1 1901 0.006 0.014 0.6 |
|
Write traj. 1 1 11 0.030 0.066 3.1 |
|
Update 1 1 1001 0.005 0.011 0.5 |
|
Constraints 1 1 1003 0.029 0.063 3.0 |
|
Rest 0.010 0.022 1.1 |
|
----------------------------------------------------------------------------- |
|
Total 0.958 2.108 100.0 |
|
----------------------------------------------------------------------------- |
|
Breakdown of PME mesh computation |
|
----------------------------------------------------------------------------- |
|
PME spread 1 1 1001 0.048 0.106 5.0 |
|
PME gather 1 1 1001 0.070 0.154 7.3 |
|
PME 3D-FFT 1 1 2002 0.032 0.070 3.3 |
|
PME solve Elec 1 1 1001 0.019 0.042 2.0 |
|
----------------------------------------------------------------------------- |
|
|
|
Core t (s) Wall t (s) (%) |
|
Time: 0.958 0.958 100.0 |
|
(ns/day) (hour/ns) |
|
Performance: 90.243 0.266 |
|
Finished mdrun on rank 0 Tue Jun 7 16:54:18 2022 |
|
|
|
|