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br_zero.log

with zero epsilon and sigma - Arthur Zalevsky, 10/30/2018 09:29 AM

 
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Log file opened on Tue Oct 30 11:27:23 2018
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Host: xwing.vsb.fbb.msu.ru  pid: 23949  rank ID: 0  number of ranks:  1
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                      :-) GROMACS - gmx mdrun, 2018.1 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
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    Par Bjelkmar    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
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Executable:   /usr/bin/gmx
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Data prefix:  /usr
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Working dir:  /home/domain/data/2016/hiv/domain_a_helix/br_fix/rotates/dih_000
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Command line:
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  gmx mdrun -deffnm br_zero
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GROMACS version:    2018.1
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Precision:          single
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Memory model:       64 bit
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MPI library:        thread_mpi
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support:        disabled
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SIMD instructions:  SSE2
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FFT library:        fftw-3.3.7-sse2-avx
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RDTSCP usage:       disabled
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TNG support:        enabled
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Hwloc support:      hwloc-1.11.6
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Tracing support:    disabled
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Built on:           2018-03-31 17:12:46
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Built by:           buildd@debian [CMAKE]
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Build OS/arch:      Linux x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Westmere E56xx/L56xx/X56xx (Nehalem-C)
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Build CPU family:   6   Model: 44   Stepping: 1
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Build CPU features: aes apic clfsh cmov cx8 cx16 intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 x2apic
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C compiler:         /usr/bin/cc GNU 7.3.0
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C compiler flags:    -msse2   -g -O2 -fdebug-prefix-map=/build/gromacs-Fqu8ou/gromacs-2018.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /usr/bin/c++ GNU 7.3.0
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C++ compiler flags:  -msse2   -g -O2 -fdebug-prefix-map=/build/gromacs-Fqu8ou/gromacs-2018.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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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) i7-6700K CPU @ 4.00GHz
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    Family: 6   Model: 94   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 (33666584576 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: 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:1b81  Class: 0x0300  Numa: 0
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      0000:00:17.0  Id: 8086:a102  Class: 0x0106  Numa: 0
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      0000:05:00.0  Id: 126f:2260  Class: 0x0108  Numa: 0
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      0000:00:1f.6  Id: 8086:15b8  Class: 0x0200  Numa: 0
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Highest SIMD level requested by all nodes in run: AVX2_256
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SIMD instructions selected at compile time:       SSE2
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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
107
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                         = 100000
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   init-step                      = 0
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   simulation-part                = 1
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   comm-mode                      = Angular
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   nstcomm                        = 100
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   bd-fric                        = 0
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   ld-seed                        = -1993099600
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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                        = 10
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   nstvout                        = 0
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   nstfout                        = 0
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   nstlog                         = 1000
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   nstcalcenergy                  = 100
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   nstenergy                      = 1000
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   nstxout-compressed             = 0
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Group
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   nstlist                        = 10
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   ns-type                        = Grid
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   pbc                            = no
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   periodic-molecules             = false
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   verlet-buffer-tolerance        = 0.005
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   rlist                          = 2
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   coulombtype                    = Cut-off
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   coulomb-modifier               = None
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   rcoulomb-switch                = 0
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   rcoulomb                       = 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                   = None
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   rvdw-switch                    = 0
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   rvdw                           = 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                     = 0
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   fourier-ny                     = 0
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   fourier-nz                     = 0
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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                   = OBC
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   nstgbradii                     = 1
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   rgbradii                       = 2
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   gb-epsilon-solvent             = 80
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   gb-saltconc                    = 0.1
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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             = 2.25936
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   tcoupl                         = V-rescale
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   nsttcouple                     = 10
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = No
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   pcoupltype                     = Isotropic
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   nstpcouple                     = -1
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   tau-p                          = 1
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   compressibility (3x3):
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      compressibility[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   ref-p (3x3):
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      ref-p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   refcoord-scaling               = No
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   posres-com (3):
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      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = false
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = false
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 4
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   lincs-iter                     = 1
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   lincs-warnangle                = 30
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   nwall                          = 0
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   wall-type                      = 9-3
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   wall-r-linpot                  = -1
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   wall-atomtype[0]               = -1
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   wall-atomtype[1]               = -1
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   wall-density[0]                = 0
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   wall-density[1]                = 0
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   wall-ewald-zfac                = 3
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   pull                           = false
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   awh                            = false
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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = No
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   disre-weighting                = Conservative
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   disre-mixed                    = false
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   dr-fc                          = 1000
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   dr-tau                         = 0
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   nstdisreout                    = 100
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   orire-fc                       = 0
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   orire-tau                      = 0
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   nstorireout                    = 100
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   free-energy                    = no
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   cos-acceleration               = 0
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   deform (3x3):
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      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   simulated-tempering            = false
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   swapcoords                     = no
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   userint1                       = 0
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   userint2                       = 0
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   userint3                       = 0
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   userint4                       = 0
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   userreal1                      = 0
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   userreal2                      = 0
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   userreal3                      = 0
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   userreal4                      = 0
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   applied-forces:
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     electric-field:
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       x:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       y:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       z:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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grpopts:
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   nrdf:     2217.66     847.341
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   ref-t:          10         400
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   tau-t:         0.1         0.1
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annealing:          No          No
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annealing-npoints:           0           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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Initializing Domain Decomposition on 8 ranks
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Dynamic load balancing: locked
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Initial maximum inter charge-group distances:
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    two-body bonded interactions: 0.421 nm, LJ-14, atoms 1534 1543
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  multi-body bonded interactions: 0.421 nm, Proper Dih., atoms 1534 1543
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Minimum cell size due to bonded interactions: 0.463 nm
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Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.768 nm
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Estimated maximum distance required for P-LINCS: 0.768 nm
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This distance will limit the DD cell size, you can override this with -rcon
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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 0.960 nm
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The maximum allowed number of cells is: X 6 Y 2 Z 2
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Domain decomposition grid 4 x 2 x 1, separate PME ranks 0
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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 Y 2
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The initial domain decomposition cell size is: X 1.55 nm Y 1.20 nm
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           2.000 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)   2.000 nm
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          multi-body bonded interactions  (-rdd)   1.201 nm
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  atoms separated by up to 5 constraints  (-rcon)  1.201 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 3 Y 1
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The minimum size for domain decomposition cells is 0.811 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 0.52 Y 0.00
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           2.000 nm
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            two-body bonded interactions  (-rdd)   2.000 nm
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          multi-body bonded interactions  (-rdd)   0.811 nm
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  atoms separated by up to 5 constraints  (-rcon)  0.811 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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NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
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removed in a future release when 'verlet' supports all interaction forms.
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System total charge: -5.000
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Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Coulomb -0e+00
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Table routines are used for coulomb: false
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Table routines are used for vdw:     false
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Cut-off's:   NS: 2   Coulomb: 2   LJ: 2
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Generated table with 1500 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1500 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1500 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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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 1591
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There are inter charge-group constraints,
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will communicate selected coordinates each lincs iteration
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Linking all bonded interactions to atoms
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Intra-simulation communication will occur every 10 steps.
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Center of mass motion removal mode is Angular
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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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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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G. Bussi, D. Donadio and M. Parrinello
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Canonical sampling through velocity rescaling
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J. Chem. Phys. 126 (2007) pp. 014101
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-------- -------- --- Thank You --- -------- --------
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There are: 1554 Atoms
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Atom distribution over 8 domains: av 194 stddev 107 min 19 max 388
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Grid: 6 x 4 x 4 cells
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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: 7.54e-06
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Initial temperature: 4.49562 K
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Started mdrun on rank 0 Tue Oct 30 11:27:23 2018
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           Step           Time
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              0        0.00000
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    1.38192e+03    3.96565e+03    1.15004e+02    1.44321e+03    2.83653e+03
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        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
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   -2.88602e+03   -2.00518e+04   -1.31955e+04    4.39752e+01   -1.31515e+04
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  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -1.31515e+04    3.45122e+00    0.00000e+00    2.06457e-04
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DD  step 9 load imb.: force 143.3%
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step 20 Turning on dynamic load balancing, because the performance loss due to load imbalance is 25.1 %.
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-------------------------------------------------------
432
Program:     gmx mdrun, version 2018.1
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Source file: src/gromacs/mdlib/nsgrid.cpp (line 635)
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MPI rank:    7 (out of 8)
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Range checking error:
437
Explanation: During neighborsearching, we assign each particle to a grid
438
based on its coordinates. If your system contains collisions or parameter
439
errors that give particles very high velocities you might end up with some
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coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
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put these on a grid, so this is usually where we detect those errors.
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Make sure your system is properly energy-minimized and that the potential
443
energy seems reasonable before trying again.
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Variable ind has value 423. It should have been within [ 0 .. 423 ]
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For more information and tips for troubleshooting, please check the GROMACS
447
website at http://www.gromacs.org/Documentation/Errors
448
-------------------------------------------------------