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616 lines
26 KiB
616 lines
26 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: 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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++++ 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
|
||
|
|
|
||
|
|
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
|
||
|
|
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: 2.82e-07
|
||
|
|
Initial temperature: 9.19637e-08 K
|
||
|
|
|
||
|
|
Started mdrun on rank 0 Tue Jun 7 16:54:17 2022
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
0 0.00000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
||
|
|
6.54106e+00 2.91333e+01 2.05991e+01 2.39229e+01 -4.72959e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-2.50213e+03 -3.84107e+02 -3.37410e+01 2.37485e+02 6.25183e+01
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-2.54450e+03 1.43772e-01 -2.54436e+03 3.41735e-02 -5.87450e+01
|
||
|
|
Pressure (bar) Constr. rmsd
|
||
|
|
-1.02412e+03 3.10957e-07
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
100 0.10000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
||
|
|
6.06172e+00 2.53319e+01 2.26869e+01 2.81504e+01 -4.76577e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-2.50754e+03 -3.93727e+02 -3.37410e+01 1.09030e+02 3.58492e+01
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-2.71266e+03 1.68273e+02 -2.54439e+03 3.99971e+01 -5.87450e+01
|
||
|
|
Pressure (bar) Constr. rmsd
|
||
|
|
-1.31114e+03 4.66734e-07
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
200 0.20000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
||
|
|
6.24788e+00 2.79298e+01 2.16709e+01 2.69609e+01 -4.75449e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-2.50610e+03 -3.69433e+02 -3.37410e+01 4.82246e+01 3.25844e+01
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-2.75041e+03 2.06001e+02 -2.54441e+03 4.89650e+01 -5.87450e+01
|
||
|
|
Pressure (bar) Constr. rmsd
|
||
|
|
-8.55580e+02 4.46975e-07
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
300 0.30000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
||
|
|
7.03768e+00 3.23298e+01 1.93120e+01 2.62972e+01 -4.76136e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-2.50757e+03 -3.48475e+02 -3.37410e+01 -1.00443e+01 4.04671e+01
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-2.77915e+03 2.34761e+02 -2.54439e+03 5.58008e+01 -5.87450e+01
|
||
|
|
Pressure (bar) Constr. rmsd
|
||
|
|
-4.48931e+02 5.61386e-07
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
400 0.40000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
||
|
|
6.35392e+00 3.06192e+01 2.04599e+01 2.71354e+01 -4.76162e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-2.50950e+03 -3.65008e+02 -3.37410e+01 -1.01754e+01 3.59214e+01
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-2.80269e+03 2.58293e+02 -2.54440e+03 6.13943e+01 -5.87450e+01
|
||
|
|
Pressure (bar) Constr. rmsd
|
||
|
|
-4.52210e+02 5.29885e-07
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
500 0.50000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
||
|
|
6.71373e+00 3.63823e+01 1.92696e+01 2.34328e+01 -4.75007e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-2.50640e+03 -3.86323e+02 -3.37410e+01 -1.36942e+01 3.75627e+01
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-2.82155e+03 2.77155e+02 -2.54439e+03 6.58776e+01 -5.87450e+01
|
||
|
|
Pressure (bar) Constr. rmsd
|
||
|
|
-4.94223e+02 5.68981e-07
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
600 0.60000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
||
|
|
7.17528e+00 3.61834e+01 1.94872e+01 2.38956e+01 -4.72431e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-2.50299e+03 -3.67483e+02 -3.37410e+01 -4.33854e+01 3.32332e+01
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-2.83235e+03 2.87970e+02 -2.54438e+03 6.84482e+01 -5.87450e+01
|
||
|
|
Pressure (bar) Constr. rmsd
|
||
|
|
-2.13021e+02 5.15836e-07
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
700 0.70000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
||
|
|
7.22778e+00 2.50161e+01 2.74334e+01 3.88358e+01 -4.81276e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-2.51810e+03 -3.79901e+02 -3.37410e+01 -3.59257e+01 3.84723e+01
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-2.83549e+03 2.91116e+02 -2.54438e+03 6.91960e+01 -5.87450e+01
|
||
|
|
Pressure (bar) Constr. rmsd
|
||
|
|
-2.15106e+02 4.83708e-07
|
||
|
|
|
||
|
|
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
|
||
|
|
|