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509 lines
21 KiB
509 lines
21 KiB
2 years ago
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:-) 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: 2570737
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Command line:
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gmx -quiet mdrun -deffnm nvt -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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++++ 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 = 2101298815
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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 = 1000
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nstcalcenergy = 100
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nstenergy = 1000
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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 = 0.005
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rlist = 0.961399
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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 = V-rescale
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nsttcouple = 10
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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: 298.15
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tau-t: 0.1
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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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Changing nstlist from 10 to 100, rlist from 0.961399 to 0.961399
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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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|
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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 980 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 980 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 980 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 100 steps, buffer 0.000 nm, rlist 0.961 nm
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At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
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|
|
updated every 100 steps, buffer 0.119 nm, rlist 1.080 nm
|
||
|
|
|
||
|
|
Using Lorentz-Berthelot Lennard-Jones combination rule
|
||
|
|
|
||
|
|
Long Range LJ corr.: <C6> 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
|
||
|
|
|