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md.log

Viveca Lindahl, 03/13/2018 04:32 PM

 
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Log file opened on Tue Mar 13 16:32:43 2018
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Host: tcbl07  pid: 2852  rank ID: 0  number of ranks:  1
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            :-) GROMACS - gmx mdrun, 2018.1-dev-20180313-3500c87 (-:
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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    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  
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  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   
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 Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    
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  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  
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  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   
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    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  
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   Michael Shirts     Alfons Sijbers     Peter Tieleman    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) 2001-2017, 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 2018.1-dev-20180313-3500c87
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Executable:   /data/viveca/gromacs/build-release-2018-debug-mpi/bin/gmx_mpi_debug
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Data prefix:  /home/viveca/gromacs (source tree)
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Working dir:  /home/viveca/tmp/test-maxh/dna/replica-0/sim-0
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Command line:
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  gmx_mpi_debug mdrun -v -stepout 1 -nstlist 1 -npme 0 -ntomp 1 -maxh 0.0001 -multidir sim-0/
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GROMACS version:    2018.1-dev-20180313-3500c87
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GIT SHA1 hash:      3500c872064c808515066bf80e699b95b38dad0f
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Branched from:      717fd5b8c0b47ab8bff70cfbd189e52a452db543 (1 newer local commits)
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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:        fftw-3.3.3-sse2-avx
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      hwloc-1.8.0
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Tracing support:    disabled
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Built on:           2018-03-01 15:39:54
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Built by:           viveca@tcbl07 [CMAKE]
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Build OS/arch:      Linux 3.13.0-141-generic x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
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Build CPU family:   6   Model: 60   Stepping: 3
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Build CPU 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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C compiler:         /usr/bin/cc GNU 4.8.4
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C compiler flags:    -march=core-avx2    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -g -fno-inline 
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C++ compiler:       /usr/bin/c++ GNU 4.8.4
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C++ compiler flags:  -march=core-avx2    -std=c++11  -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations -Wall  -g -fno-inline 
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Running on 1 node with total 4 cores, 8 logical cores
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Hardware detected on host tcbl07 (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) Core(TM) i7-4770 CPU @ 3.40GHz
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    Family: 6   Model: 60   Stepping: 3
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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   4] [   1   5] [   2   6] [   3   7]
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    Numa nodes:
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      Node  0 (16764940288 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. 8, shared 2 ways
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      L3: 8388608 bytes, linesize 64 bytes, assoc. 16, shared 8 ways
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    PCI devices:
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      0000:01:00.0  Id: 10de:1187  Class: 0x0300  Numa: 0
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      0000:03:00.0  Id: 10ec:8168  Class: 0x0200  Numa: 0
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      0000:00:1f.2  Id: 8086:8c02  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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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                         = 100000000
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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                        = -1148593145
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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                         = 5000000
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   nstcalcenergy                  = 100
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   nstenergy                      = 50000
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   nstxout-compressed             = 500000
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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
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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
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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
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   DispCorr                       = EnerPres
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   table-extension                = 1
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   fourierspacing                 = 0.121
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   fourier-nx                     = 36
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   fourier-ny                     = 36
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   fourier-nz                     = 36
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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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   implicit-solvent               = No
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   gb-algorithm                   = Still
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   nstgbradii                     = 1
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   rgbradii                       = 1
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   gb-epsilon-solvent             = 80
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   gb-saltconc                    = 0
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   gb-obc-alpha                   = 1
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   gb-obc-beta                    = 0.8
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   gb-obc-gamma                   = 4.85
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   gb-dielectric-offset           = 0.009
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   sa-algorithm                   = Ace-approximation
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   sa-surface-tension             = 2.05016
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   tcoupl                         = V-rescale
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   nsttcouple                     = 10
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = Parrinello-Rahman
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   pcoupltype                     = Isotropic
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   nstpcouple                     = 10
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   tau-p                          = 5
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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:       11070
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   ref-t:         300
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   tau-t:         0.5
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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 1, rlist from 1 to 1
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This is simulation 0 out of 1 running as a composite GROMACS
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multi-simulation job. Setup for this simulation:
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Using 1 MPI process
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Using 1 OpenMP thread 
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