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:-) GROMACS - gmx mdrun, 2019.1 (-:
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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
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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) 2001-2018, 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 2019.1
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Executable: /apps/broadwell/centos7/GROMACS/2019.1-intel-2018b-UArecipe/bin/gmx_mpi
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Data prefix: /apps/broadwell/centos7/GROMACS/2019.1-intel-2018b-UArecipe
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Working dir: /scratch/gromacs-2019/2018u3-2019.2
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Process ID: 13456
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Command line:
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gmx_mpi mdrun -ntomp 1 -s 0519.tpr -o /scratch/gromacs-2019/2018u3-2019.2/0519.trr -x /scratch/gromacs-2019/2018u3-2019.2/0519.xtc -cpo /scratch/gromacs-2019/2018u3-2019.2/0519.cpt -c /scratch/gromacs-2019/2018u3-2019.2/0519.gro -e /scratch/gromacs-2019/2018u3-2019.2/0519.edr -dhdl /scratch/gromacs-2019/2018u3-2019.2/0519.xvg -g /scratch/gromacs-2019/2018u3-2019.2/0519.log -px /scratch/gromacs-2019/2018u3-2019.2/0519.x.xvg -pf /scratch/gromacs-2019/2018u3-2019.2/0519.f.xvg -noconfout -rcon 0.7 -pin on -dds 0.9 -dlb auto -maxh 1
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GROMACS version: 2019.1
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Precision: single
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Memory model: 64 bit
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MPI library: 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: AVX2_256
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FFT library: Intel MKL
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RDTSCP usage: enabled
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TNG support: enabled
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Hwloc support: hwloc-1.11.8
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Tracing support: disabled
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C compiler: /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicc Intel 18.0.3.20180410
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C compiler flags: -march=core-avx2 -mkl=sequential -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
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C++ compiler: /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicpc Intel 18.0.3.20180410
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C++ compiler flags: -march=core-avx2 -mkl=sequential -std=c++11 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits
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Running on 1 node with total 28 cores, 28 logical cores
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Hardware detected on host r2c10cn4 (the node of MPI rank 0):
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CPU info:
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Vendor: Intel
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Brand: Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
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Family: 6 Model: 79 Stepping: 1
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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 pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt 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] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13]
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Socket 1: [ 14] [ 15] [ 16] [ 17] [ 18] [ 19] [ 20] [ 21] [ 22] [ 23] [ 24] [ 25] [ 26] [ 27]
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Numa nodes:
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Node 0 (68600541184 bytes mem): 0 1 2 3 4 5 6 7 8 9 10 11 12 13
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Node 1 (68719476736 bytes mem): 14 15 16 17 18 19 20 21 22 23 24 25 26 27
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Latency:
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0 1
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0 1.00 2.10
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1 2.10 1.00
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Caches:
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L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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L3: 36700160 bytes, linesize 64 bytes, assoc. 20, shared 14 ways
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PCI devices:
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0000:01:00.0 Id: 8086:1521 Class: 0x0200 Numa: 0
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0000:01:00.1 Id: 8086:1521 Class: 0x0200 Numa: 0
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0000:02:00.0 Id: 15b3:1013 Class: 0x0207 Numa: 0
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0000:00:11.4 Id: 8086:8d62 Class: 0x0106 Numa: 0
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0000:07:00.0 Id: 1a03:2000 Class: 0x0300 Numa: 0
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0000:00:1f.2 Id: 8086:8d02 Class: 0x0106 Numa: 0
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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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++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
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https://doi.org/10.5281/zenodo.2564764
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-------- -------- --- Thank You --- -------- --------
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Input Parameters:
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integrator = md
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tinit = 0
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dt = 0.002
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nsteps = 500000
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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 = -1437393019
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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 = 0
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nstvout = 0
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nstfout = 0
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nstlog = 50000
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nstcalcenergy = 100
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nstenergy = 50000
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nstxout-compressed = 50000
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compressed-x-precision = 1000
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cutoff-scheme = Verlet
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nstlist = 20
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ns-type = Grid
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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 = 1.223
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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 = 1.2
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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 = 1
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rvdw = 1.2
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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 = 96
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fourier-ny = 84
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fourier-nz = 80
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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 = 20
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nh-chain-length = 0
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print-nose-hoover-chain-variables = false
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pcoupl = Berendsen
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pcoupltype = Isotropic
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nstpcouple = 20
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tau-p = 2
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compressibility (3x3):
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compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
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compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
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compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
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ref-p (3x3):
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ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
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ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
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refcoord-scaling = COM
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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 = true
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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 = true
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pull-cylinder-r = 1.5
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pull-constr-tol = 1e-06
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pull-print-COM = true
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pull-print-ref-value = true
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pull-print-components = true
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pull-nstxout = 50000
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pull-nstfout = 50000
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pull-pbc-ref-prev-step-com = false
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pull-xout-average = false
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pull-fout-average = false
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pull-ngroups = 3
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pull-group 0:
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atom: not available
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weight: not available
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pbcatom = -1
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pull-group 1:
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atom (1):
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atom[0]=1442
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weight: not available
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pbcatom = -1
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pull-group 2:
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atom (2):
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atom[0]=4641
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atom[1]=4643
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weight: not available
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pbcatom = 4641
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pull-ncoords = 1
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pull-coord 0:
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type = umbrella
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geometry = distance
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group[0] = 1
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group[1] = 2
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dim (3):
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dim[0]=1
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dim[1]=1
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dim[2]=1
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origin (3):
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origin[0]= 0.00000e+00
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origin[1]= 0.00000e+00
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origin[2]= 0.00000e+00
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vec (3):
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vec[0]= 0.00000e+00
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vec[1]= 0.00000e+00
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vec[2]= 0.00000e+00
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start = true
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init = 0.518654
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rate = 0
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k = 1000
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kB = 1000
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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
|
|
325
|
applied-forces:
|
|
326
|
electric-field:
|
|
327
|
x:
|
|
328
|
E0 = 0
|
|
329
|
omega = 0
|
|
330
|
t0 = 0
|
|
331
|
sigma = 0
|
|
332
|
y:
|
|
333
|
E0 = 0
|
|
334
|
omega = 0
|
|
335
|
t0 = 0
|
|
336
|
sigma = 0
|
|
337
|
z:
|
|
338
|
E0 = 0
|
|
339
|
omega = 0
|
|
340
|
t0 = 0
|
|
341
|
sigma = 0
|
|
342
|
grpopts:
|
|
343
|
nrdf: 12909.9 439152
|
|
344
|
ref-t: 300 300
|
|
345
|
tau-t: 0.1 0.1
|
|
346
|
annealing: No No
|
|
347
|
annealing-npoints: 0 0
|
|
348
|
acc: 0 0 0
|
|
349
|
nfreeze: N N N
|
|
350
|
energygrp-flags[ 0]: 0
|
|
351
|
|
|
352
|
Changing nstlist from 20 to 80, rlist from 1.223 to 1.326
|
|
353
|
|
|
354
|
|
|
355
|
Initializing Domain Decomposition on 28 ranks
|
|
356
|
Dynamic load balancing: locked
|
|
357
|
Minimum cell size due to atom displacement: 0.514 nm
|
|
358
|
Initial maximum distances in bonded interactions:
|
|
359
|
two-body bonded interactions: 0.443 nm, LJ-14, atoms 1990 2780
|
|
360
|
multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1990 2780
|
|
361
|
Minimum cell size due to bonded interactions: 0.487 nm
|
|
362
|
User supplied maximum distance required for P-LINCS: 0.700 nm
|
|
363
|
Guess for relative PME load: 0.13
|
|
364
|
Will use 24 particle-particle and 4 PME only ranks
|
|
365
|
This is a guess, check the performance at the end of the log file
|
|
366
|
Using 4 separate PME ranks, as guessed by mdrun
|
|
367
|
Scaling the initial minimum size with 1/0.9 (option -dds) = 1.11111
|
|
368
|
Optimizing the DD grid for 24 cells with a minimum initial size of 0.778 nm
|
|
369
|
The maximum allowed number of cells is: X 18 Y 17 Z 15
|
|
370
|
Domain decomposition grid 4 x 3 x 2, separate PME ranks 4
|
|
371
|
PME domain decomposition: 4 x 1 x 1
|
|
372
|
Interleaving PP and PME ranks
|
|
373
|
This rank does only particle-particle work.
|
|
374
|
Domain decomposition rank 0, coordinates 0 0 0
|
|
375
|
|
|
376
|
The initial number of communication pulses is: X 1 Y 1 Z 1
|
|
377
|
The initial domain decomposition cell size is: X 3.63 nm Y 4.41 nm Z 6.01 nm
|
|
378
|
|
|
379
|
The maximum allowed distance for atoms involved in interactions is:
|
|
380
|
non-bonded interactions 1.326 nm
|
|
381
|
(the following are initial values, they could change due to box deformation)
|
|
382
|
two-body bonded interactions (-rdd) 1.326 nm
|
|
383
|
multi-body bonded interactions (-rdd) 1.326 nm
|
|
384
|
atoms separated by up to 5 constraints (-rcon) 3.628 nm
|
|
385
|
|
|
386
|
When dynamic load balancing gets turned on, these settings will change to:
|
|
387
|
The maximum number of communication pulses is: X 1 Y 1 Z 1
|
|
388
|
The minimum size for domain decomposition cells is 1.326 nm
|
|
389
|
The requested allowed shrink of DD cells (option -dds) is: 0.90
|
|
390
|
The allowed shrink of domain decomposition cells is: X 0.37 Y 0.30 Z 0.22
|
|
391
|
The maximum allowed distance for atoms involved in interactions is:
|
|
392
|
non-bonded interactions 1.326 nm
|
|
393
|
two-body bonded interactions (-rdd) 1.326 nm
|
|
394
|
multi-body bonded interactions (-rdd) 1.326 nm
|
|
395
|
atoms separated by up to 5 constraints (-rcon) 1.326 nm
|
|
396
|
|
|
397
|
Using 28 MPI processes
|
|
398
|
Using 1 OpenMP thread per MPI process
|
|
399
|
|
|
400
|
|
|
401
|
Overriding thread affinity set outside gmx mdrun
|
|
402
|
|
|
403
|
Pinning threads with an auto-selected logical core stride of 1
|
|
404
|
System total charge: -0.000
|
|
405
|
Will do PME sum in reciprocal space for electrostatic interactions.
|
|
406
|
|
|
407
|
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
|
|
408
|
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
|
|
409
|
A smooth particle mesh Ewald method
|
|
410
|
J. Chem. Phys. 103 (1995) pp. 8577-8592
|
|
411
|
-------- -------- --- Thank You --- -------- --------
|
|
412
|
|
|
413
|
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
|
|
414
|
Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -8.333e-06
|
|
415
|
Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
|
|
416
|
|
|
417
|
Long Range LJ corr.: <C6> 3.1361e-04
|
|
418
|
Generated table with 1163 data points for Ewald.
|
|
419
|
Tabscale = 500 points/nm
|
|
420
|
Generated table with 1163 data points for LJ6.
|
|
421
|
Tabscale = 500 points/nm
|
|
422
|
Generated table with 1163 data points for LJ12.
|
|
423
|
Tabscale = 500 points/nm
|
|
424
|
Generated table with 1163 data points for 1-4 COUL.
|
|
425
|
Tabscale = 500 points/nm
|
|
426
|
Generated table with 1163 data points for 1-4 LJ6.
|
|
427
|
Tabscale = 500 points/nm
|
|
428
|
Generated table with 1163 data points for 1-4 LJ12.
|
|
429
|
Tabscale = 500 points/nm
|
|
430
|
|
|
431
|
Using SIMD 4x8 nonbonded short-range kernels
|
|
432
|
|
|
433
|
Using a dual 4x8 pair-list setup updated with dynamic pruning:
|
|
434
|
outer list: updated every 80 steps, buffer 0.126 nm, rlist 1.326 nm
|
|
435
|
inner list: updated every 13 steps, buffer 0.002 nm, rlist 1.202 nm
|
|
436
|
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
|
|
437
|
outer list: updated every 80 steps, buffer 0.275 nm, rlist 1.475 nm
|
|
438
|
inner list: updated every 13 steps, buffer 0.052 nm, rlist 1.252 nm
|
|
439
|
|
|
440
|
Using full Lennard-Jones parameter combination matrix
|
|
441
|
|
|
442
|
|
|
443
|
Will apply potential COM pulling
|
|
444
|
with 1 pull coordinate and 2 groups
|
|
445
|
Pull group 1: 1 atoms, mass 13.019
|
|
446
|
Pull group 2: 2 atoms, mass 26.018
|
|
447
|
|
|
448
|
Initializing Parallel LINear Constraint Solver
|
|
449
|
|
|
450
|
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
|
|
451
|
B. Hess
|
|
452
|
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
|
|
453
|
J. Chem. Theory Comput. 4 (2008) pp. 116-122
|
|
454
|
-------- -------- --- Thank You --- -------- --------
|
|
455
|
|
|
456
|
The number of constraints is 1073
|
|
457
|
There are constraints between atoms in different decomposition domains,
|
|
458
|
will communicate selected coordinates each lincs iteration
|
|
459
|
|
|
460
|
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
|
|
461
|
S. Miyamoto and P. A. Kollman
|
|
462
|
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
|
|
463
|
Water Models
|
|
464
|
J. Comp. Chem. 13 (1992) pp. 952-962
|
|
465
|
-------- -------- --- Thank You --- -------- --------
|
|
466
|
|
|
467
|
|
|
468
|
Linking all bonded interactions to atoms
|
|
469
|
|
|
470
|
|
|
471
|
The -noconfout functionality is deprecated, and may be removed in a future version.
|
|
472
|
|
|
473
|
Intra-simulation communication will occur every 20 steps.
|
|
474
|
Center of mass motion removal mode is Linear
|
|
475
|
We have the following groups for center of mass motion removal:
|
|
476
|
0: rest
|
|
477
|
|
|
478
|
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
|
|
479
|
G. Bussi, D. Donadio and M. Parrinello
|
|
480
|
Canonical sampling through velocity rescaling
|
|
481
|
J. Chem. Phys. 126 (2007) pp. 014101
|
|
482
|
-------- -------- --- Thank You --- -------- --------
|
|
483
|
|
|
484
|
There are: 224238 Atoms
|
|
485
|
Atom distribution over 24 domains: av 9343 stddev 159 min 8986 max 9487
|
|
486
|
|
|
487
|
Started mdrun on rank 0 Mon Apr 29 17:41:50 2019
|
|
488
|
|
|
489
|
Step Time
|
|
490
|
0 0.00000
|
|
491
|
|
|
492
|
Energies (kJ/mol)
|
|
493
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
494
|
5.09961e+03 7.77425e+03 4.85656e+03 2.47900e+03 -1.61705e+02
|
|
495
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
496
|
6.64263e+04 5.11422e+05 -1.65591e+04 -3.68724e+06 1.05263e+04
|
|
497
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
498
|
6.82855e-14 -3.09538e+06 9.65238e+03 -3.08573e+06 -3.08550e+06
|
|
499
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
500
|
5.13609e+00 -1.19286e+02 -1.38955e+03 2.44768e-06
|
|
501
|
|
|
502
|
|
|
503
|
DD step 79 load imb.: force 1.0% pme mesh/force 0.641
|
|
504
|
|
|
505
|
DD step 49999 load imb.: force 0.1% pme mesh/force 0.636
|
|
506
|
Step Time
|
|
507
|
50000 100.00000
|
|
508
|
|
|
509
|
Energies (kJ/mol)
|
|
510
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
511
|
5.07309e+03 7.88547e+03 4.77681e+03 2.53831e+03 -1.25494e+02
|
|
512
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
513
|
6.62515e+04 5.14346e+05 -1.65502e+04 -3.69187e+06 1.06637e+04
|
|
514
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
515
|
2.05921e+00 -3.09701e+06 5.65433e+05 -2.53158e+06 -3.10370e+06
|
|
516
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
517
|
3.00870e+02 -1.19158e+02 6.88380e+00 2.90667e-06
|
|
518
|
|
|
519
|
Writing checkpoint, step 51600 at Mon Apr 29 17:56:51 2019
|
|
520
|
|
|
521
|
|
|
522
|
|
|
523
|
DD step 99999 load imb.: force 0.1% pme mesh/force 0.629
|
|
524
|
Step Time
|
|
525
|
100000 200.00000
|
|
526
|
|
|
527
|
Energies (kJ/mol)
|
|
528
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
529
|
4.83947e+03 7.76333e+03 5.02919e+03 2.57352e+03 -2.01676e+02
|
|
530
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
531
|
6.63908e+04 5.11349e+05 -1.65637e+04 -3.68742e+06 1.05885e+04
|
|
532
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
533
|
8.22999e+00 -3.09564e+06 5.64535e+05 -2.53111e+06 -3.10244e+06
|
|
534
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
535
|
3.00392e+02 -1.19353e+02 -1.15791e+01 2.85825e-06
|
|
536
|
|
|
537
|
Writing checkpoint, step 103200 at Mon Apr 29 18:11:51 2019
|
|
538
|
|
|
539
|
|
|
540
|
|
|
541
|
DD step 149999 load imb.: force 0.1% pme mesh/force 0.629
|
|
542
|
Step Time
|
|
543
|
150000 300.00000
|
|
544
|
|
|
545
|
Energies (kJ/mol)
|
|
546
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
547
|
4.73493e+03 7.51411e+03 4.79377e+03 2.62355e+03 -1.61440e+02
|
|
548
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
549
|
6.65032e+04 5.13268e+05 -1.65593e+04 -3.69267e+06 1.06059e+04
|
|
550
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
551
|
1.06595e+01 -3.09934e+06 5.61731e+05 -2.53761e+06 -3.10114e+06
|
|
552
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
553
|
2.98900e+02 -1.19289e+02 3.20921e+01 2.72740e-06
|
|
554
|
|
|
555
|
Writing checkpoint, step 154720 at Mon Apr 29 18:26:50 2019
|
|
556
|
|
|
557
|
|
|
558
|
|
|
559
|
DD step 199999 load imb.: force 0.1% pme mesh/force 0.629
|
|
560
|
Step Time
|
|
561
|
200000 400.00000
|
|
562
|
|
|
563
|
Energies (kJ/mol)
|
|
564
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
565
|
4.72977e+03 7.77913e+03 4.97781e+03 2.64590e+03 -1.86805e+02
|
|
566
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
567
|
6.65539e+04 5.12121e+05 -1.65476e+04 -3.68970e+06 1.06055e+04
|
|
568
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
569
|
1.13379e+01 -3.09701e+06 5.63238e+05 -2.53377e+06 -3.09980e+06
|
|
570
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
571
|
2.99702e+02 -1.19120e+02 7.92175e-01 2.82831e-06
|
|
572
|
|
|
573
|
|
|
574
|
Step 204240: Run time exceeded 0.990 hours, will terminate the run within 80 steps
|
|
575
|
Step Time
|
|
576
|
204320 408.64000
|
|
577
|
|
|
578
|
Energies (kJ/mol)
|
|
579
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
580
|
4.92980e+03 7.61687e+03 4.96679e+03 2.53375e+03 -3.05528e+02
|
|
581
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
582
|
6.64921e+04 5.13116e+05 -1.65538e+04 -3.69267e+06 1.05618e+04
|
|
583
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
584
|
1.42167e+01 -3.09930e+06 5.64881e+05 -2.53442e+06 -3.09968e+06
|
|
585
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
586
|
3.00577e+02 -1.19210e+02 -2.00279e+01 2.79905e-06
|
|
587
|
|
|
588
|
<====== ############### ==>
|
|
589
|
<==== A V E R A G E S ====>
|
|
590
|
<== ############### ======>
|
|
591
|
|
|
592
|
Statistics over 204321 steps using 2044 frames
|
|
593
|
|
|
594
|
Energies (kJ/mol)
|
|
595
|
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
|
|
596
|
4.92036e+03 7.68631e+03 4.89835e+03 2.55049e+03 -1.99119e+02
|
|
597
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
598
|
6.64616e+04 5.13012e+05 -1.65583e+04 -3.69162e+06 1.06089e+04
|
|
599
|
COM Pull En. Potential Kinetic En. Total Energy Conserved En.
|
|
600
|
6.17256e+00 -3.09823e+06 5.63468e+05 -2.53476e+06 -3.10236e+06
|
|
601
|
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
|
|
602
|
2.99824e+02 -1.19275e+02 2.23477e-01 0.00000e+00
|
|
603
|
|
|
604
|
Box-X Box-Y Box-Z
|
|
605
|
1.45131e+01 1.32260e+01 1.20181e+01
|
|
606
|
|
|
607
|
Total Virial (kJ/mol)
|
|
608
|
1.87654e+05 7.26374e+01 1.12804e+02
|
|
609
|
6.93176e+01 1.87756e+05 -2.64689e+01
|
|
610
|
1.08856e+02 -2.62935e+01 1.88012e+05
|
|
611
|
|
|
612
|
Pressure (bar)
|
|
613
|
2.26382e+00 -1.00341e+00 -1.46889e+00
|
|
614
|
-9.55656e-01 1.18775e+00 2.94279e-01
|
|
615
|
-1.41206e+00 2.91779e-01 -2.78115e+00
|
|
616
|
|
|
617
|
T-protein_and_gpfT-water_and_ions
|
|
618
|
2.99917e+02 2.99822e+02
|
|
619
|
|
|
620
|
|
|
621
|
M E G A - F L O P S A C C O U N T I N G
|
|
622
|
|
|
623
|
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
|
|
624
|
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
|
|
625
|
W3=SPC/TIP3p W4=TIP4p (single or pairs)
|
|
626
|
V&F=Potential and force V=Potential only F=Force only
|
|
627
|
|
|
628
|
Computing: M-Number M-Flops % Flops
|
|
629
|
-----------------------------------------------------------------------------
|
|
630
|
Pair Search distance check 314388.467106 2829496.204 0.1
|
|
631
|
NxN Ewald Elec. + LJ [F] 20746621.748032 1369277035.370 51.0
|
|
632
|
NxN Ewald Elec. + LJ [V&F] 209746.607680 22442887.022 0.8
|
|
633
|
NxN LJ [F] 27932.911872 921786.092 0.0
|
|
634
|
NxN LJ [V&F] 282.407584 12143.526 0.0
|
|
635
|
NxN Ewald Elec. [F] 19665342.884864 1199585915.977 44.6
|
|
636
|
NxN Ewald Elec. [V&F] 198815.960544 16700540.686 0.6
|
|
637
|
1,4 nonbonded interactions 1499.511819 134956.064 0.0
|
|
638
|
Calc Weights 137449.597194 4948185.499 0.2
|
|
639
|
Spread Q Bspline 2932258.073472 5864516.147 0.2
|
|
640
|
Gather F Bspline 2932258.073472 17593548.441 0.7
|
|
641
|
3D-FFT 5087717.535810 40701740.286 1.5
|
|
642
|
Solve PME 1647.644544 105449.251 0.0
|
|
643
|
Reset In Box 572.703852 1718.112 0.0
|
|
644
|
CG-CoM 572.928090 1718.784 0.0
|
|
645
|
Bonds 755.579058 44579.164 0.0
|
|
646
|
Angles 1436.172309 241276.948 0.0
|
|
647
|
Propers 670.377201 153516.379 0.0
|
|
648
|
Impropers 525.922254 109391.829 0.0
|
|
649
|
Virial 2302.074006 41437.332 0.0
|
|
650
|
Stop-CM 458.342472 4583.425 0.0
|
|
651
|
P-Coupling 2291.039646 13746.238 0.0
|
|
652
|
Calc-Ekin 4582.079292 123716.141 0.0
|
|
653
|
Lincs 229.643530 13778.612 0.0
|
|
654
|
Lincs-Mat 393.726732 1574.907 0.0
|
|
655
|
Constraint-V 48026.130248 384209.042 0.0
|
|
656
|
Constraint-Vir 2390.046330 57361.112 0.0
|
|
657
|
Settle 15855.614396 5121363.450 0.2
|
|
658
|
-----------------------------------------------------------------------------
|
|
659
|
Total 2687432172.038 100.0
|
|
660
|
-----------------------------------------------------------------------------
|
|
661
|
|
|
662
|
|
|
663
|
D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
|
|
664
|
|
|
665
|
av. #atoms communicated per step for force: 2 x 246696.7
|
|
666
|
av. #atoms communicated per step for LINCS: 2 x 13446.5
|
|
667
|
|
|
668
|
|
|
669
|
Dynamic load balancing report:
|
|
670
|
DLB was off during the run due to low measured imbalance.
|
|
671
|
Average load imbalance: 0.1%.
|
|
672
|
The balanceable part of the MD step is 94%, load imbalance is computed from this.
|
|
673
|
Part of the total run time spent waiting due to load imbalance: 0.1%.
|
|
674
|
Average PME mesh/force load: 0.626
|
|
675
|
Part of the total run time spent waiting due to PP/PME imbalance: 5.0 %
|
|
676
|
|
|
677
|
NOTE: 5.0 % performance was lost because the PME ranks
|
|
678
|
had less work to do than the PP ranks.
|
|
679
|
You might want to decrease the number of PME ranks
|
|
680
|
or decrease the cut-off and the grid spacing.
|
|
681
|
|
|
682
|
|
|
683
|
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
|
|
684
|
|
|
685
|
On 24 MPI ranks doing PP, and
|
|
686
|
on 4 MPI ranks doing PME
|
|
687
|
|
|
688
|
Computing: Num Num Call Wall time Giga-Cycles
|
|
689
|
Ranks Threads Count (s) total sum %
|
|
690
|
-----------------------------------------------------------------------------
|
|
691
|
Domain decomp. 24 1 2554 16.469 948.609 0.4
|
|
692
|
DD comm. load 24 1 30 0.000 0.018 0.0
|
|
693
|
Send X to PME 24 1 204321 25.447 1465.761 0.6
|
|
694
|
Neighbor search 24 1 2555 51.089 2942.769 1.2
|
|
695
|
Comm. coord. 24 1 201766 37.600 2165.797 0.9
|
|
696
|
Force 24 1 204321 3146.792 181257.095 75.6
|
|
697
|
Wait + Comm. F 24 1 204321 23.666 1363.155 0.6
|
|
698
|
PME mesh * 4 1 204321 2080.840 19976.273 8.3
|
|
699
|
PME wait for PP * 1485.242 14258.471 5.9
|
|
700
|
Wait + Recv. PME F 24 1 204321 17.680 1018.379 0.4
|
|
701
|
NB X/F buffer ops. 24 1 607853 28.278 1628.805 0.7
|
|
702
|
COM pull force 24 1 204321 153.254 8827.496 3.7
|
|
703
|
Write traj. 24 1 8 0.032 1.829 0.0
|
|
704
|
Update 24 1 204321 23.097 1330.399 0.6
|
|
705
|
Constraints 24 1 204321 38.073 2193.007 0.9
|
|
706
|
Comm. energies 24 1 10217 0.472 27.187 0.0
|
|
707
|
Rest 4.167 240.005 0.1
|
|
708
|
-----------------------------------------------------------------------------
|
|
709
|
Total 3566.114 239645.361 100.0
|
|
710
|
-----------------------------------------------------------------------------
|
|
711
|
(*) Note that with separate PME ranks, the walltime column actually sums to
|
|
712
|
twice the total reported, but the cycle count total and % are correct.
|
|
713
|
-----------------------------------------------------------------------------
|
|
714
|
Breakdown of PME mesh computation
|
|
715
|
-----------------------------------------------------------------------------
|
|
716
|
PME redist. X/F 4 1 408642 166.921 1602.456 0.7
|
|
717
|
PME spread 4 1 204321 789.959 7583.685 3.2
|
|
718
|
PME gather 4 1 204321 481.080 4618.417 1.9
|
|
719
|
PME 3D-FFT 4 1 408642 535.328 5139.201 2.1
|
|
720
|
PME 3D-FFT Comm. 4 1 408642 58.858 565.038 0.2
|
|
721
|
PME solve Elec 4 1 204321 47.900 459.842 0.2
|
|
722
|
-----------------------------------------------------------------------------
|
|
723
|
|
|
724
|
Core t (s) Wall t (s) (%)
|
|
725
|
Time: 99851.151 3566.114 2800.0
|
|
726
|
59:26
|
|
727
|
(ns/day) (hour/ns)
|
|
728
|
Performance: 9.901 2.424
|
|
729
|
Finished mdrun on rank 0 Mon Apr 29 18:41:16 2019
|
|
730
|
|