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md_3355steps.log

Paul Bauer, 07/08/2019 01:43 PM

 
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          :-) GROMACS - gmx mdrun, 2019.4-dev-20190702-1a90d02500 (-:
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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 2019.4-dev-20190702-1a90d02500
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Executable:   /home/acmnpv/data/gerrit/2019/install-clang-7/bin/gmx
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Data prefix:  /home/acmnpv/data/gerrit/2019/install-clang-7
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Working dir:  /home/acmnpv/data/bugs/2950
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Process ID:   19024
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Command line:
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  gmx mdrun -s topol.tpr
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GROMACS version:    2019.4-dev-20190702-1a90d02500
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GIT SHA1 hash:      1a90d02500cda09aa5d4da99cf71e6bc212e26e7
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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:     disabled
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GPU support:        disabled
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SIMD instructions:  NONE
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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-1.11.11
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Tracing support:    disabled
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C compiler:         /usr/bin/clang-7 Clang 7.0.1
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C compiler flags:       -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wno-unknown-pragmas  -g 
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C++ compiler:       /usr/bin/clang++-7 Clang 7.0.1
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C++ compiler flags:     -std=c++11  -Wdeprecated -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-prototypes -Wall -Wno-unknown-pragmas  -g 
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Running on 1 node with total 4 cores, 8 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) Core(TM) i5-8250U CPU @ 1.60GHz
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    Family: 6   Model: 142   Stepping: 10
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp 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   4] [   1   5] [   2   6] [   3   7]
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    Numa nodes:
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      Node  0 (8068657152 bytes mem):   0   1   2   3   4   5   6   7
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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. 4, shared 2 ways
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      L3: 6291456 bytes, linesize 64 bytes, assoc. 12, shared 8 ways
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    PCI devices:
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      0000:00:02.0  Id: 8086:5917  Class: 0x0300  Numa: 0
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      0000:02:00.0  Id: 168c:003e  Class: 0x0280  Numa: 0
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      0000:6e:00.0  Id: 144d:a808  Class: 0x0108  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:       None
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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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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                         = 3333
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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                        = -1834598251
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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                         = 100
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   nstcalcenergy                  = 100
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   nstenergy                      = 100
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   nstxout-compressed             = 100
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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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   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                          = 1.2
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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                    = 0
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   rvdw                           = 1.2
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.12
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   fourier-nx                     = 64
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   fourier-ny                     = 64
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   fourier-nz                     = 64
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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                         = Nose-Hoover
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   nsttcouple                     = 10
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   nh-chain-length                = 1
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = Parrinello-Rahman
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   pcoupltype                     = Isotropic
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   nstpcouple                     = 10
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   tau-p                          = 10
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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               = 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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grpopts:
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   nrdf:       86397
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   ref-t:      298.15
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   tau-t:           2
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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 1.2 to 1.223
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Initializing Domain Decomposition on 8 ranks
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Dynamic load balancing: locked
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Minimum cell size due to atom displacement: 0.485 nm
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Initial maximum distances in bonded interactions:
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    two-body bonded interactions: 0.302 nm, LJ-14, atoms 33914 33918
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  multi-body bonded interactions: 0.302 nm, Ryckaert-Bell., atoms 33914 33918
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Minimum cell size due to bonded interactions: 0.332 nm
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Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm
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Estimated maximum distance required for P-LINCS: 0.218 nm
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Using 0 separate PME ranks, as there are too few total
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 ranks for efficient splitting
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Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
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Optimizing the DD grid for 8 cells with a minimum initial size of 0.606 nm
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The maximum allowed number of cells is: X 12 Y 12 Z 12
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Domain decomposition grid 8 x 1 x 1, separate PME ranks 0
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PME domain decomposition: 8 x 1 x 1
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Domain decomposition rank 0, coordinates 0 0 0
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The initial number of communication pulses is: X 2
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The initial domain decomposition cell size is: X 0.94 nm
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The maximum allowed distance for atoms involved in interactions is:
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                 non-bonded interactions           1.223 nm
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(the following are initial values, they could change due to box deformation)
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            two-body bonded interactions  (-rdd)   1.223 nm
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          multi-body bonded interactions  (-rdd)   0.937 nm
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              virtual site constructions  (-rcon)  0.937 nm
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  atoms separated by up to 5 constraints  (-rcon)  0.937 nm
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When dynamic load balancing gets turned on, these settings will change to:
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The maximum number of communication pulses is: X 2
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The minimum size for domain decomposition cells is 0.619 nm
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The requested allowed shrink of DD cells (option -dds) is: 0.80
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The allowed shrink of domain decomposition cells is: X 0.66
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The maximum allowed distance for atoms involved in interactions is:
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                 non-bonded interactions           1.223 nm
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            two-body bonded interactions  (-rdd)   1.223 nm
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          multi-body bonded interactions  (-rdd)   0.619 nm
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              virtual site constructions  (-rcon)  0.619 nm
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  atoms separated by up to 5 constraints  (-rcon)  0.619 nm
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Using 8 MPI threads
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Pinning threads with an auto-selected logical core stride of 1
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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 0.384195 nm for Ewald
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Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -8.333e-06
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Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
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Generated table with 1111 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1111 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1111 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Using plain C 4x4 nonbonded short-range kernels
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WARNING: Using the slow plain C kernels. This should
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not happen during routine usage on supported platforms.
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Using a dual 4x4 pair-list setup updated with dynamic pruning:
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  outer list: updated every 100 steps, buffer 0.023 nm, rlist 1.223 nm
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  inner list: updated every  63 steps, buffer 0.001 nm, rlist 1.201 nm
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At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
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  outer list: updated every 100 steps, buffer 0.165 nm, rlist 1.365 nm
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  inner list: updated every  63 steps, buffer 0.113 nm, rlist 1.313 nm
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Using geometric Lennard-Jones combination rule
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Removing pbc first time
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Initializing Parallel LINear Constraint Solver
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess
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P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 116-122
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-------- -------- --- Thank You --- -------- --------
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The number of constraints is 19200
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There are constraints between atoms in different decomposition domains,
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will communicate selected coordinates each lincs iteration
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Miyamoto and P. A. Kollman
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SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
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Water Models
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J. Comp. Chem. 13 (1992) pp. 952-962
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-------- -------- --- Thank You --- -------- --------
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Linking all bonded interactions to atoms
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There are 32000 inter charge-group virtual sites,
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will an extra communication step for selected coordinates and forces
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Intra-simulation communication will occur every 10 steps.
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Center of mass motion removal mode is Linear
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We have the following groups for center of mass motion removal:
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  0:  rest
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There are: 38400 Atoms
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There are: 8000 VSites
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Atom distribution over 8 domains: av 5800 stddev 53 min 5725 max 5882
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Constraining the starting coordinates (step 0)
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Constraining the coordinates at t0-dt (step 0)
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RMS relative constraint deviation after constraining: 1.52e-06
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Initial temperature: 297.372 K
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Started mdrun on rank 0 Mon Jul  8 11:55:48 2019
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           Step           Time
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              0        0.00000
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   Energies (kJ/mol)
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           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
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    6.13937e+03    3.73980e+04    6.95260e+03    0.00000e+00    6.86985e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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   -8.57153e+03   -2.93805e+05    2.69644e+03   -1.80491e+05    1.06708e+05
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -7.37835e+04   -7.37582e+04    2.97094e+02   -1.52949e+02    1.80806e-06
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DD  step 99 load imb.: force  8.1%
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           Step           Time
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            100        0.10000
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   Energies (kJ/mol)
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           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
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    6.08921e+03    3.69553e+04    6.99494e+03    0.00000e+00    6.87329e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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   -8.46819e+03   -2.93581e+05    2.68826e+03   -1.80589e+05    1.06784e+05
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -7.38051e+04   -7.37807e+04    2.97305e+02    3.47333e+01    1.82472e-06
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DD  step 199 load imb.: force  5.4%
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step 200 Turning on dynamic load balancing, because the performance loss due to load imbalance is 5.3 %.
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           Step           Time
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            200        0.20000
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   Energies (kJ/mol)
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           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
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    6.05544e+03    3.68973e+04    6.82000e+03    0.00000e+00    6.86826e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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   -8.36552e+03   -2.93579e+05    2.68921e+03   -1.80800e+05    1.07031e+05
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -7.37683e+04   -7.37785e+04    2.97995e+02    8.38627e+01    1.82336e-06
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DD  step 299  vol min/aver 0.983  load imb.: force  4.1%
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           Step           Time
466
            300        0.30000
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   Energies (kJ/mol)
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           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
470
    6.11371e+03    3.68604e+04    6.82124e+03    0.00000e+00    6.86390e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
472
   -7.32241e+03   -2.94138e+05    2.72681e+03   -1.80300e+05    1.06623e+05
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -7.36766e+04   -7.37726e+04    2.96857e+02    7.53353e+01    1.83336e-06
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477
DD  step 399  vol min/aver 0.977  load imb.: force  8.0%
478
           Step           Time
479
            400        0.40000
480

    
481
   Energies (kJ/mol)
482
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
483
    6.31331e+03    3.70298e+04    6.84294e+03    0.00000e+00    6.86549e+04
484
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
485
   -7.97884e+03   -2.94682e+05    2.67384e+03   -1.81146e+05    1.07595e+05
486
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
487
   -7.35518e+04   -7.37723e+04    2.99563e+02   -1.24245e+02    1.81175e-06
488

    
489

    
490
DD  step 499  vol min/aver 0.961  load imb.: force 11.6%
491
           Step           Time
492
            500        0.50000
493

    
494
   Energies (kJ/mol)
495
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
496
    6.12771e+03    3.72460e+04    6.64468e+03    0.00000e+00    6.87303e+04
497
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
498
   -8.93524e+03   -2.92948e+05    2.72204e+03   -1.80413e+05    1.06975e+05
499
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
500
   -7.34382e+04   -7.37708e+04    2.97837e+02   -2.25737e+01    1.82216e-06
501

    
502

    
503
DD  step 599  vol min/aver 0.970  load imb.: force  5.0%
504
           Step           Time
505
            600        0.60000
506

    
507
   Energies (kJ/mol)
508
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
509
    6.10932e+03    3.72207e+04    6.93729e+03    0.00000e+00    6.86747e+04
510
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
511
   -8.01216e+03   -2.94429e+05    2.65890e+03   -1.80840e+05    1.07518e+05
512
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
513
   -7.33221e+04   -7.37792e+04    2.99349e+02    3.87122e+00    1.79143e-06
514

    
515

    
516
DD  step 699  vol min/aver 0.981  load imb.: force 12.4%
517
           Step           Time
518
            700        0.70000
519

    
520
   Energies (kJ/mol)
521
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
522
    6.17206e+03    3.68629e+04    7.07521e+03    0.00000e+00    6.86665e+04
523
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
524
   -8.38800e+03   -2.93948e+05    2.64517e+03   -1.80914e+05    1.07677e+05
525
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
526
   -7.32370e+04   -7.37834e+04    2.99792e+02   -6.32657e+01    1.80767e-06
527

    
528

    
529
DD  step 799  vol min/aver 0.945  load imb.: force 10.6%
530
           Step           Time
531
            800        0.80000
532

    
533
   Energies (kJ/mol)
534
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
535
    6.23219e+03    3.69298e+04    6.85208e+03    0.00000e+00    6.86978e+04
536
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
537
   -8.32756e+03   -2.93873e+05    2.67264e+03   -1.80816e+05    1.07627e+05
538
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
539
   -7.31896e+04   -7.37915e+04    2.99652e+02   -3.32506e+02    1.80669e-06
540

    
541

    
542
DD  step 899  vol min/aver 0.976  load imb.: force  4.8%
543
           Step           Time
544
            900        0.90000
545

    
546
   Energies (kJ/mol)
547
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
548
    6.27008e+03    3.71884e+04    6.89608e+03    0.00000e+00    6.86574e+04
549
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
550
   -8.14604e+03   -2.94118e+05    2.59132e+03   -1.80660e+05    1.07464e+05
551
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
552
   -7.31964e+04   -7.37840e+04    2.99199e+02   -9.59544e+01    1.82368e-06
553

    
554

    
555
DD  step 999  vol min/aver 0.978  load imb.: force  1.8%
556
           Step           Time
557
           1000        1.00000
558

    
559
   Energies (kJ/mol)
560
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
561
    6.26241e+03    3.70113e+04    6.93059e+03    0.00000e+00    6.86962e+04
562
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
563
   -7.98159e+03   -2.94497e+05    2.68213e+03   -1.80896e+05    1.07544e+05
564
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
565
   -7.33517e+04   -7.37959e+04    2.99423e+02    2.21988e+02    1.79843e-06
566

    
567

    
568
DD  step 1099  vol min/aver 0.980  load imb.: force  2.0%
569
           Step           Time
570
           1100        1.10000
571

    
572
   Energies (kJ/mol)
573
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
574
    6.17443e+03    3.67686e+04    7.15314e+03    0.00000e+00    6.86406e+04
575
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
576
   -7.86733e+03   -2.94897e+05    2.69107e+03   -1.81336e+05    1.07717e+05
577
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
578
   -7.36188e+04   -7.38049e+04    2.99905e+02   -4.17458e+01    1.81966e-06
579

    
580

    
581
DD  step 1199  vol min/aver 0.971  load imb.: force  3.4%
582
           Step           Time
583
           1200        1.20000
584

    
585
   Energies (kJ/mol)
586
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
587
    6.24247e+03    3.71543e+04    6.81282e+03    0.00000e+00    6.87047e+04
588
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
589
   -8.18210e+03   -2.93692e+05    2.70018e+03   -1.80260e+05    1.06320e+05
590
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
591
   -7.39399e+04   -7.37996e+04    2.96014e+02   -3.22987e+02    1.80645e-06
592

    
593

    
594
DD  step 1299  vol min/aver 0.983  load imb.: force  2.8%
595
           Step           Time
596
           1300        1.30000
597

    
598
   Energies (kJ/mol)
599
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
600
    6.10643e+03    3.71429e+04    6.83784e+03    0.00000e+00    6.86898e+04
601
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
602
   -8.88385e+03   -2.93421e+05    2.65320e+03   -1.80875e+05    1.06667e+05
603
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
604
   -7.42072e+04   -7.37953e+04    2.96981e+02   -1.82535e+02    1.80261e-06
605

    
606

    
607
DD  step 1399  vol min/aver 0.980  load imb.: force  1.1%
608
           Step           Time
609
           1400        1.40000
610

    
611
Writing checkpoint, step 1400 at Mon Jul  8 12:11:02 2019
612

    
613

    
614
   Energies (kJ/mol)
615
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
616
    5.96913e+03    3.70902e+04    6.84084e+03    0.00000e+00    6.86412e+04
617
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
618
   -7.97913e+03   -2.94526e+05    2.69998e+03   -1.81264e+05    1.06839e+05
619
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
620
   -7.44254e+04   -7.37945e+04    2.97458e+02    1.19125e+02    1.81380e-06
621

    
622

    
623
DD  step 1499  vol min/aver 0.976  load imb.: force  1.4%
624
           Step           Time
625
           1500        1.50000
626

    
627
   Energies (kJ/mol)
628
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
629
    5.92097e+03    3.69985e+04    6.85927e+03    0.00000e+00    6.87640e+04
630
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
631
   -7.95846e+03   -2.94648e+05    2.70575e+03   -1.81358e+05    1.06716e+05
632
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
633
   -7.46426e+04   -7.38033e+04    2.97116e+02    1.54741e+02    1.79588e-06
634

    
635

    
636
DD  step 1599  vol min/aver 0.979  load imb.: force  5.5%
637
           Step           Time
638
           1600        1.60000
639

    
640
   Energies (kJ/mol)
641
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
642
    6.18337e+03    3.68869e+04    7.01802e+03    0.00000e+00    6.86584e+04
643
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
644
   -7.42501e+03   -2.95396e+05    2.62283e+03   -1.81452e+05    1.06647e+05
645
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
646
   -7.48048e+04   -7.38009e+04    2.96924e+02   -9.20138e+01    1.81699e-06
647

    
648

    
649
DD  step 1699  vol min/aver 0.974  load imb.: force  8.3%
650
           Step           Time
651
           1700        1.70000
652

    
653
   Energies (kJ/mol)
654
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
655
    6.04581e+03    3.71368e+04    6.78759e+03    0.00000e+00    6.86486e+04
656
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
657
   -8.92117e+03   -2.93325e+05    2.68280e+03   -1.80945e+05    1.06041e+05
658
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
659
   -7.49032e+04   -7.37902e+04    2.95238e+02   -1.83311e+02    1.80451e-06
660

    
661

    
662
DD  step 1799  vol min/aver 0.936  load imb.: force  4.3%
663
           Step           Time
664
           1800        1.80000
665

    
666
   Energies (kJ/mol)
667
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
668
    5.96715e+03    3.70631e+04    6.63354e+03    0.00000e+00    6.87330e+04
669
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
670
   -8.35654e+03   -2.93725e+05    2.63533e+03   -1.81050e+05    1.06159e+05
671
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
672
   -7.48910e+04   -7.37854e+04    2.95565e+02    2.17105e+02    1.81779e-06
673

    
674

    
675
DD  step 1899  vol min/aver 0.915  load imb.: force  2.1%
676
           Step           Time
677
           1900        1.90000
678

    
679
   Energies (kJ/mol)
680
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
681
    6.06559e+03    3.73697e+04    6.87474e+03    0.00000e+00    6.86978e+04
682
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
683
   -7.90500e+03   -2.94335e+05    2.63802e+03   -1.80594e+05    1.05839e+05
684
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
685
   -7.47551e+04   -7.37777e+04    2.94675e+02    1.17299e+02    1.83411e-06
686

    
687

    
688
DD  step 1999  vol min/aver 0.906  load imb.: force  5.6%
689
           Step           Time
690
           2000        2.00000
691

    
692
   Energies (kJ/mol)
693
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
694
    6.02668e+03    3.69437e+04    6.90809e+03    0.00000e+00    6.87053e+04
695
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
696
   -7.80954e+03   -2.94806e+05    2.67212e+03   -1.81360e+05    1.06823e+05
697
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
698
   -7.45369e+04   -7.37837e+04    2.97413e+02   -4.63534e+00    1.80576e-06
699

    
700

    
701
DD  step 2099  vol min/aver 0.924  load imb.: force  3.3%
702
           Step           Time
703
           2100        2.10000
704

    
705
   Energies (kJ/mol)
706
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
707
    6.08957e+03    3.68257e+04    6.69261e+03    0.00000e+00    6.86521e+04
708
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
709
   -9.06569e+03   -2.93203e+05    2.64821e+03   -1.81360e+05    1.07113e+05
710
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
711
   -7.42474e+04   -7.37870e+04    2.98222e+02   -1.95065e+02    1.79135e-06
712

    
713

    
714
DD  step 2199  vol min/aver 0.936  load imb.: force  1.7%
715
           Step           Time
716
           2200        2.20000
717

    
718
   Energies (kJ/mol)
719
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
720
    6.12033e+03    3.73695e+04    6.92732e+03    0.00000e+00    6.86844e+04
721
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
722
   -8.45085e+03   -2.92907e+05    2.64009e+03   -1.79616e+05    1.05739e+05
723
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
724
   -7.38767e+04   -7.37704e+04    2.94397e+02   -4.00863e+01    1.81394e-06
725

    
726

    
727
DD  step 2299  vol min/aver 0.937  load imb.: force  5.2%
728
           Step           Time
729
           2300        2.30000
730

    
731
   Energies (kJ/mol)
732
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
733
    6.14098e+03    3.72168e+04    7.05835e+03    0.00000e+00    6.87211e+04
734
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
735
   -8.55558e+03   -2.93604e+05    2.60115e+03   -1.80421e+05    1.06960e+05
736
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
737
   -7.34607e+04   -7.37784e+04    2.97797e+02    3.11599e+01    1.80724e-06
738

    
739

    
740
DD  step 2399  vol min/aver 0.922  load imb.: force  5.1%
741
           Step           Time
742
           2400        2.40000
743

    
744
   Energies (kJ/mol)
745
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
746
    6.24848e+03    3.68294e+04    7.04009e+03    0.00000e+00    6.86804e+04
747
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
748
   -8.13035e+03   -2.93776e+05    2.66037e+03   -1.80448e+05    1.07377e+05
749
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
750
   -7.30706e+04   -7.37882e+04    2.98958e+02    8.30692e+00    1.79928e-06
751

    
752

    
753
DD  step 2499  vol min/aver 0.898  load imb.: force  8.8%
754
           Step           Time
755
           2500        2.50000
756

    
757
   Energies (kJ/mol)
758
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
759
    6.25848e+03    3.71577e+04    7.10200e+03    0.00000e+00    6.86577e+04
760
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
761
   -8.17789e+03   -2.93320e+05    2.65270e+03   -1.79670e+05    1.06960e+05
762
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
763
   -7.27103e+04   -7.37854e+04    2.97794e+02   -1.22955e+02    1.83178e-06
764

    
765

    
766
DD  step 2599  vol min/aver 0.937  load imb.: force  3.9%
767
           Step           Time
768
           2600        2.60000
769

    
770
   Energies (kJ/mol)
771
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
772
    6.18966e+03    3.72015e+04    7.07821e+03    0.00000e+00    6.87287e+04
773
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
774
   -8.75011e+03   -2.93342e+05    2.67072e+03   -1.80224e+05    1.07790e+05
775
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
776
   -7.24334e+04   -7.37919e+04    3.00107e+02   -7.60742e+01    1.82195e-06
777

    
778

    
779
DD  step 2699  vol min/aver 0.955  load imb.: force 10.0%
780
           Step           Time
781
           2700        2.70000
782

    
783
   Energies (kJ/mol)
784
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
785
    6.24284e+03    3.71064e+04    6.98447e+03    0.00000e+00    6.86231e+04
786
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
787
   -8.47707e+03   -2.92826e+05    2.69760e+03   -1.79649e+05    1.07345e+05
788
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
789
   -7.23031e+04   -7.37991e+04    2.98869e+02    1.36919e+02    1.81265e-06
790

    
791

    
792
DD  step 2799  vol min/aver 0.960  load imb.: force 17.6%
793
           Step           Time
794
           2800        2.80000
795

    
796
   Energies (kJ/mol)
797
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
798
    5.88247e+03    3.70408e+04    6.92215e+03    0.00000e+00    6.86923e+04
799
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
800
   -7.87749e+03   -2.93892e+05    2.68568e+03   -1.80546e+05    1.08210e+05
801
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
802
   -7.23368e+04   -7.38139e+04    3.01275e+02    1.57450e+02    1.82820e-06
803

    
804

    
805
DD  step 2899  vol min/aver 0.920  load imb.: force 14.0%
806
           Step           Time
807
           2900        2.90000
808

    
809
   Energies (kJ/mol)
810
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
811
    6.20975e+03    3.73964e+04    6.95009e+03    0.00000e+00    6.86858e+04
812
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
813
   -7.79352e+03   -2.93768e+05    2.65963e+03   -1.79660e+05    1.07149e+05
814
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
815
   -7.25118e+04   -7.38077e+04    2.98321e+02   -9.60734e+01    1.81186e-06
816

    
817

    
818
DD  step 2999  vol min/aver 0.903  load imb.: force  5.0%
819
           Step           Time
820
           3000        3.00000
821

    
822
   Energies (kJ/mol)
823
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
824
    5.90471e+03    3.74609e+04    7.02023e+03    0.00000e+00    6.86692e+04
825
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
826
   -8.55846e+03   -2.93155e+05    2.70897e+03   -1.79949e+05    1.07110e+05
827
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
828
   -7.28389e+04   -7.38218e+04    2.98214e+02   -7.00275e+01    1.80699e-06
829

    
830

    
831
DD  step 3099  vol min/aver 0.939  load imb.: force 13.2%
832
           Step           Time
833
           3100        3.10000
834

    
835
Writing checkpoint, step 3100 at Mon Jul  8 12:26:35 2019
836

    
837

    
838
   Energies (kJ/mol)
839
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
840
    6.00399e+03    3.70506e+04    6.84256e+03    0.00000e+00    6.87138e+04
841
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
842
   -8.64508e+03   -2.93292e+05    2.76162e+03   -1.80565e+05    1.07359e+05
843
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
844
   -7.32057e+04   -7.38369e+04    2.98906e+02    2.38772e+02    1.80492e-06
845

    
846

    
847
DD  step 3199  vol min/aver 0.950  load imb.: force  2.9%
848
           Step           Time
849
           3200        3.20000
850

    
851
   Energies (kJ/mol)
852
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
853
    5.93713e+03    3.69215e+04    6.89552e+03    0.00000e+00    6.86979e+04
854
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
855
   -8.86544e+03   -2.93600e+05    2.72125e+03   -1.81292e+05    1.07716e+05
856
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
857
   -7.35766e+04   -7.38406e+04    2.99900e+02    4.77583e+01    1.82692e-06
858

    
859

    
860
DD  step 3299  vol min/aver 0.963  load imb.: force  1.5%
861
           Step           Time
862
           3300        3.30000
863

    
864
   Energies (kJ/mol)
865
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
866
    6.02165e+03    3.66924e+04    6.91272e+03    0.00000e+00    6.86431e+04
867
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
868
   -8.36343e+03   -2.94284e+05    2.69534e+03   -1.81682e+05    1.07687e+05
869
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
870
   -7.39951e+04   -7.38454e+04    2.99819e+02   -1.47526e+02    1.82528e-06
871

    
872
           Step           Time
873
           3333        3.33300
874

    
875
Writing checkpoint, step 3333 at Mon Jul  8 12:28:26 2019
876

    
877

    
878

    
879

    
880
-----------------------------------------------------------
881
Restarting from checkpoint, appending to previous log file.
882

    
883
           :-) GROMACS - gmx mdrun, 2019.4-dev-20190702-1a90d0250 (-:
884

    
885
Executable:   /nethome/pbauer/data/bugs/2950/../../gerrit/release-2019/build-gcc-8/bin/gmx
886
Data prefix:  /nethome/pbauer/data/gerrit/release-2019 (source tree)
887
Working dir:  /nethome/pbauer/data/bugs/2950
888
Process ID:   3245532
889
Command line:
890
  gmx mdrun -s 3355.tpr -cpi state.cpt
891

    
892
GROMACS version:    2019.4-dev-20190702-1a90d0250
893
GIT SHA1 hash:      1a90d02500cda09aa5d4da99cf71e6bc212e26e7
894
Precision:          single
895
Memory model:       64 bit
896
MPI library:        thread_mpi
897
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
898
GPU support:        disabled
899
SIMD instructions:  NONE
900
FFT library:        fftw-3.3.7-sse2-avx
901
RDTSCP usage:       disabled
902
TNG support:        enabled
903
Hwloc support:      disabled
904
Tracing support:    disabled
905
C compiler:         /opt/tcbsys/gcc/8.1/bin/gcc-8 GNU 8.1.0
906
C compiler flags:       -Werror=stringop-truncation -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -g -fno-inline 
907
C++ compiler:       /opt/tcbsys/gcc/8.1/bin/g++-8 GNU 8.1.0
908
C++ compiler flags:     -std=c++11  -Wstringop-truncation -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations -Wall  -g -fno-inline 
909

    
910
Changing nstlist from 10 to 100, rlist from 1.2 to 1.223
911

    
912

    
913
Initializing Domain Decomposition on 32 ranks
914
Dynamic load balancing: locked
915
Minimum cell size due to atom displacement: 0.485 nm
916
Initial maximum distances in bonded interactions:
917
    two-body bonded interactions: 0.301 nm, LJ-14, atoms 16652 16656
918
  multi-body bonded interactions: 0.301 nm, Ryckaert-Bell., atoms 16652 16656
919
Minimum cell size due to bonded interactions: 0.331 nm
920
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm
921
Estimated maximum distance required for P-LINCS: 0.218 nm
922
Guess for relative PME load: 0.04
923
Will use 30 particle-particle and 2 PME only ranks
924
This is a guess, check the performance at the end of the log file
925
Using 2 separate PME ranks, as guessed by mdrun
926
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
927
Optimizing the DD grid for 30 cells with a minimum initial size of 0.606 nm
928
The maximum allowed number of cells is: X 12 Y 12 Z 12
929
Domain decomposition grid 5 x 3 x 2, separate PME ranks 2
930
PME domain decomposition: 2 x 1 x 1
931
Interleaving PP and PME ranks
932
This rank does only particle-particle work.
933
Domain decomposition rank 0, coordinates 0 0 0
934

    
935
The initial number of communication pulses is: X 1 Y 1 Z 1
936
The initial domain decomposition cell size is: X 1.50 nm Y 2.50 nm Z 3.74 nm
937

    
938
The maximum allowed distance for atoms involved in interactions is:
939
                 non-bonded interactions           1.223 nm
940
(the following are initial values, they could change due to box deformation)
941
            two-body bonded interactions  (-rdd)   1.223 nm
942
          multi-body bonded interactions  (-rdd)   1.223 nm
943
              virtual site constructions  (-rcon)  1.498 nm
944
  atoms separated by up to 5 constraints  (-rcon)  1.498 nm
945

    
946
When dynamic load balancing gets turned on, these settings will change to:
947
The maximum number of communication pulses is: X 2 Y 2 Z 1
948
The minimum size for domain decomposition cells is 0.899 nm
949
The requested allowed shrink of DD cells (option -dds) is: 0.80
950
The allowed shrink of domain decomposition cells is: X 0.60 Y 0.36 Z 0.33
951
The maximum allowed distance for atoms involved in interactions is:
952
                 non-bonded interactions           1.223 nm
953
            two-body bonded interactions  (-rdd)   1.223 nm
954
          multi-body bonded interactions  (-rdd)   0.899 nm
955
              virtual site constructions  (-rcon)  0.899 nm
956
  atoms separated by up to 5 constraints  (-rcon)  0.899 nm
957

    
958
Using 32 MPI threads
959
Using 1 OpenMP thread per tMPI thread
960

    
961
Pinning threads with an auto-selected logical core stride of 1
962
System total charge: -0.000
963
Will do PME sum in reciprocal space for electrostatic interactions.
964

    
965
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
966
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
967
A smooth particle mesh Ewald method
968
J. Chem. Phys. 103 (1995) pp. 8577-8592
969
-------- -------- --- Thank You --- -------- --------
970

    
971
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
972
Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -8.333e-06
973
Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
974

    
975
Generated table with 1111 data points for 1-4 COUL.
976
Tabscale = 500 points/nm
977
Generated table with 1111 data points for 1-4 LJ6.
978
Tabscale = 500 points/nm
979
Generated table with 1111 data points for 1-4 LJ12.
980
Tabscale = 500 points/nm
981

    
982
Using plain C 4x4 nonbonded short-range kernels
983

    
984
WARNING: Using the slow plain C kernels. This should
985
not happen during routine usage on supported platforms.
986

    
987
Using a dual 4x4 pair-list setup updated with dynamic pruning:
988
  outer list: updated every 100 steps, buffer 0.023 nm, rlist 1.223 nm
989
  inner list: updated every  63 steps, buffer 0.001 nm, rlist 1.201 nm
990
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
991
  outer list: updated every 100 steps, buffer 0.166 nm, rlist 1.366 nm
992
  inner list: updated every  63 steps, buffer 0.113 nm, rlist 1.313 nm
993

    
994
Using geometric Lennard-Jones combination rule
995

    
996

    
997
Initializing Parallel LINear Constraint Solver
998

    
999
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
1000
B. Hess
1001
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
1002
J. Chem. Theory Comput. 4 (2008) pp. 116-122
1003
-------- -------- --- Thank You --- -------- --------
1004

    
1005
The number of constraints is 19200
1006
There are constraints between atoms in different decomposition domains,
1007
will communicate selected coordinates each lincs iteration
1008

    
1009
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
1010
S. Miyamoto and P. A. Kollman
1011
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
1012
Water Models
1013
J. Comp. Chem. 13 (1992) pp. 952-962
1014
-------- -------- --- Thank You --- -------- --------
1015

    
1016

    
1017
Linking all bonded interactions to atoms
1018
There are 32000 inter charge-group virtual sites,
1019
will an extra communication step for selected coordinates and forces
1020

    
1021

    
1022
Intra-simulation communication will occur every 10 steps.
1023
Center of mass motion removal mode is Linear
1024
We have the following groups for center of mass motion removal:
1025
  0:  rest
1026
There are: 38400 Atoms
1027
There are: 8000 VSites
1028
Atom distribution over 30 domains: av 1546 stddev 57 min 1481 max 1615
1029

    
1030
Started mdrun on rank 0 Mon Jul  8 13:37:04 2019
1031

    
1032
           Step           Time
1033
           3355        3.35500
1034

    
1035
Writing checkpoint, step 3355 at Mon Jul  8 13:37:08 2019
1036

    
1037

    
1038
                  1958.220      28198.365 100.0
1039
-----------------------------------------------------------------------------
1040
 Breakdown of PME mesh computation
1041
-----------------------------------------------------------------------------
1042
 PME redist. X/F        8    1       6668     223.253       3214.838  11.4
1043
 PME spread             8    1       3334      20.886        300.761   1.1
1044
 PME gather             8    1       3334      30.342        436.930   1.5
1045
 PME 3D-FFT             8    1       6668       4.065         58.534   0.2
1046
 PME 3D-FFT Comm.       8    1       6668       8.992        129.479   0.5
1047
 PME solve Elec         8    1       3334       5.791         83.394   0.3
1048
-----------------------------------------------------------------------------
1049

    
1050
               Core t (s)   Wall t (s)        (%)
1051
       Time:    15665.754     1958.220      800.0
1052
                         32:38
1053
                 (ns/day)    (hour/ns)
1054
Performance:        0.147      163.152
1055
Finished mdrun on rank 0 Mon Jul  8 12:28:27 2019
1056

    
1057
   Energies (kJ/mol)
1058
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
1059
    5.87965e+03    3.71328e+04    6.73000e+03    0.00000e+00    6.87208e+04
1060
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
1061
   -8.25315e+03   -2.94160e+05    2.65487e+03   -1.81295e+05    1.66365e+06
1062
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
1063
    1.48235e+06    1.48278e+06    4.63189e+03    4.11956e+04    1.81575e-06
1064

    
1065
	<======  ###############  ==>
1066
	<====  A V E R A G E S  ====>
1067
	<==  ###############  ======>
1068

    
1069
	Statistics over 3356 steps using 34 frames
1070

    
1071
   Energies (kJ/mol)
1072
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
1073
    6.11285e+03    3.70713e+04    6.90941e+03    0.00000e+00    6.86842e+04
1074
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
1075
   -8.27930e+03   -2.93863e+05    2.67504e+03   -1.80689e+05    1.07054e+05
1076
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
1077
   -7.36357e+04   -7.37932e+04    2.98057e+02   -2.11207e+01    0.00000e+00
1078

    
1079
          Box-X          Box-Y          Box-Z
1080
    7.49476e+00    7.49476e+00    7.49476e+00
1081

    
1082
   Total Virial (kJ/mol)
1083
    3.62238e+04    2.54493e+02    6.97656e+02
1084
    2.49154e+02    3.57106e+04    4.44430e+02
1085
    6.93875e+02    4.45269e+02    3.59234e+04
1086

    
1087
   Pressure (bar)
1088
   -4.16979e+01   -1.89825e+01   -5.48333e+01
1089
   -1.85614e+01   -5.65587e+00   -3.71526e+01
1090
   -5.45353e+01   -3.72187e+01   -1.60085e+01
1091

    
1092

    
1093
	M E G A - F L O P S   A C C O U N T I N G
1094

    
1095
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
1096
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
1097
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
1098
 V&F=Potential and force  V=Potential only  F=Force only
1099

    
1100
 Computing:                               M-Number         M-Flops  % Flops
1101
-----------------------------------------------------------------------------
1102
 Pair Search distance check              18.824150         169.417     0.5
1103
 NxN QSTab Elec. + LJ [F]               505.269600       20716.054    64.0
1104
 NxN QSTab Elec. + LJ [V&F]              22.966800        1355.041     4.2
1105
 NxN LJ [F]                               0.907104          29.934     0.1
1106
 NxN LJ [V&F]                             0.041232           1.773     0.0
1107
 NxN QSTab Elec. [F]                    203.836864        6930.453    21.4
1108
 NxN QSTab Elec. [V&F]                    9.265312         379.878     1.2
1109
 1,4 nonbonded interactions               0.331200          29.808     0.1
1110
 Calc Weights                             3.201600         115.258     0.4
1111
 Spread Q Bspline                        68.300800         136.602     0.4
1112
 Gather F Bspline                        68.300800         409.805     1.3
1113
 3D-FFT                                 217.055232        1736.442     5.4
1114
 Solve PME                                0.094208           6.029     0.0
1115
 CG-CoM                                   0.046400           0.139     0.0
1116
 Bonds                                    0.110400           6.514     0.0
1117
 Angles                                   0.772800         129.830     0.4
1118
 RB-Dihedrals                             0.331200          81.806     0.3
1119
 Virial                                   0.143250           2.579     0.0
1120
 Calc-Ekin                                0.278400           7.517     0.0
1121
 Lincs                                    0.506023          30.361     0.1
1122
 Lincs-Mat                                4.669092          18.676     0.1
1123
 Constraint-V                             1.258583          10.069     0.0
1124
 Constraint-Vir                           0.098160           2.356     0.0
1125
 Settle                                   0.082179          26.544     0.1
1126
 Virtual Site 3                           0.083200           3.078     0.0
1127
 Virtual Site N                           0.748800          11.232     0.0
1128
-----------------------------------------------------------------------------
1129
 Total                                                   32347.195   100.0
1130
-----------------------------------------------------------------------------
1131

    
1132

    
1133
    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
1134

    
1135
 av. #atoms communicated per step for force:  2 x 108843.0
1136
 av. #atoms communicated per step for vsites: 3 x 2669.0
1137
 av. #atoms communicated per step for LINCS:  2 x 5128.0
1138

    
1139

    
1140
     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
1141

    
1142
On 30 MPI ranks doing PP, and
1143
on 2 MPI ranks doing PME
1144

    
1145
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
1146
                     Ranks Threads  Count      (s)         total sum    %
1147
-----------------------------------------------------------------------------
1148
 Vsite constr.         30    1         23       0.086          5.417   2.2
1149
 Send X to PME         30    1         23       0.001          0.078   0.0
1150
 Neighbor search       30    1          1       0.051          3.188   1.3
1151
 Comm. coord.          30    1         22       0.016          1.005   0.4
1152
 Force                 30    1         23       3.111        195.969  79.8
1153
 Wait + Comm. F        30    1         23       0.184         11.594   4.7
1154
 PME mesh *             2    1         23       1.611          6.765   2.8
1155
 PME wait for PP *                              2.041          8.571   3.5
1156
 Wait + Recv. PME F    30    1         23       0.001          0.066   0.0
1157
 NB X/F buffer ops.    30    1         67       0.006          0.349   0.1
1158
 Vsite spread          30    1         26       0.041          2.577   1.0
1159
 Write traj.           30    1          1       0.015          0.955   0.4
1160
 Update                30    1         23       0.004          0.224   0.1
1161
 Constraints           30    1         23       0.134          8.431   3.4
1162
 Comm. energies        30    1          3       0.000          0.013   0.0
1163
 Rest                                           0.004          0.223   0.1
1164
-----------------------------------------------------------------------------
1165
 Total                                          3.653        245.430 100.0
1166
-----------------------------------------------------------------------------
1167
(*) Note that with separate PME ranks, the walltime column actually sums to
1168
    twice the total reported, but the cycle count total and % are correct.
1169
-----------------------------------------------------------------------------
1170
 Breakdown of PME mesh computation
1171
-----------------------------------------------------------------------------
1172
 PME redist. X/F        2    1         46       0.049          0.204   0.1
1173
 PME spread             2    1         23       0.518          2.173   0.9
1174
 PME gather             2    1         23       0.765          3.213   1.3
1175
 PME 3D-FFT             2    1         46       0.121          0.510   0.2
1176
 PME 3D-FFT Comm.       2    1         46       0.004          0.016   0.0
1177
 PME solve Elec         2    1         23       0.154          0.648   0.3
1178
-----------------------------------------------------------------------------
1179

    
1180
               Core t (s)   Wall t (s)        (%)
1181
       Time:      116.855        3.653     3199.1
1182
                 (ns/day)    (hour/ns)
1183
Performance:        0.544       44.115
1184
Finished mdrun on rank 0 Mon Jul  8 13:37:08 2019
1185