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Energy minimisation .log-file - Maxim Brodmerkel, 04/25/2019 10:11 AM

 
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Log file opened on Wed Apr 24 12:47:04 2019
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Host: r95.uppmax.uu.se  pid: 337  rank ID: 0  number of ranks:  1
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                      :-) GROMACS - gmx mdrun, 2018.6 (-:
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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 2018.6
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Executable:   /sw/apps/gromacs/2018.6/rackham/bin/gmx
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Data prefix:  /sw/apps/gromacs/2018.6/rackham
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Working dir:  /crex/proj/snic2018-3-476/Maxim/Virus_capsids/STNV/2-em
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Command line:
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  gmx mdrun -v -deffnm em
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GROMACS version:    2018.6
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Precision:          single
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Memory model:       64 bit
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MPI library:        none
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OpenMP support:     disabled
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GPU support:        disabled
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SIMD instructions:  AVX2_256
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FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      hwloc-1.11.8
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Tracing support:    disabled
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Built on:           2019-03-06 13:05:31
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Built by:           pmitev@rackham3.uppmax.uu.se [CMAKE]
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Build OS/arch:      Linux 3.10.0-957.5.1.el7.x86_64 x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz
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Build CPU family:   6   Model: 79   Stepping: 1
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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:         /sw/comp/intel/compilers_and_libraries_2018.3.222/linux/bin/intel64/icc Intel 18.0.3.20180410
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C compiler flags:    -march=core-avx2    -std=gnu99 -wd3180  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits  
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C++ compiler:       /sw/comp/intel/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc Intel 18.0.3.20180410
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C++ compiler flags:  -march=core-avx2    -std=c++11  -wd3180  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits  
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Running on 1 node with total 20 cores, 20 logical cores
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Hardware detected:
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  CPU info:
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    Vendor: Intel
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    Brand:  Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz
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    Family: 6   Model: 79   Stepping: 1
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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  Hardware topology: Full, with devices
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    Sockets, cores, and logical processors:
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      Socket  0: [   0] [   1] [   2] [   3] [   4] [   5] [   6] [   7] [   8] [   9]
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      Socket  1: [  10] [  11] [  12] [  13] [  14] [  15] [  16] [  17] [  18] [  19]
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    Numa nodes:
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      Node  0 (68297416704 bytes mem):   0   1   2   3   4   5   6   7   8   9
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      Node  1 (68719476736 bytes mem):  10  11  12  13  14  15  16  17  18  19
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      Latency:
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               0     1
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         0  1.00  2.10
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         1  2.10  1.00
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    Caches:
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      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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      L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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      L3: 26214400 bytes, linesize 64 bytes, assoc. 20, shared 10 ways
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    PCI devices:
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      0000:02:00.0  Id: 15b3:1003  Class: 0x0280  Numa: 0
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      0000:00:11.4  Id: 8086:8d62  Class: 0x0106  Numa: 0
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      0000:06:00.0  Id: 19e5:1711  Class: 0x0300  Numa: 0
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      0000:00:1f.2  Id: 8086:8d02  Class: 0x0106  Numa: 0
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      0000:81:00.0  Id: 8086:1521  Class: 0x0200  Numa: 1
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      0000:81:00.1  Id: 8086:1521  Class: 0x0200  Numa: 1
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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                     = steep
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   tinit                          = 0
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   dt                             = 0.001
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   nsteps                         = 10000
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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                        = 475527610
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   emtol                          = 1000
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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                         = 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                        = 0
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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                          = 0
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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                       = 0
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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                           = 0
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.16
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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                   = 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                         = No
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   nsttcouple                     = -1
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = No
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   pcoupltype                     = Isotropic
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   nstpcouple                     = -1
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   tau-p                          = 1
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   compressibility (3x3):
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      compressibility[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   ref-p (3x3):
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      ref-p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   refcoord-scaling               = No
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   posres-com (3):
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      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = false
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = false
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 4
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   lincs-iter                     = 1
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   lincs-warnangle                = 30
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   nwall                          = 0
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   wall-type                      = 9-3
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   wall-r-linpot                  = -1
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   wall-atomtype[0]               = -1
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   wall-atomtype[1]               = -1
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   wall-density[0]                = 0
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   wall-density[1]                = 0
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   wall-ewald-zfac                = 3
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   pull                           = false
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   awh                            = false
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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = No
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   disre-weighting                = Conservative
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   disre-mixed                    = false
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   dr-fc                          = 1000
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   dr-tau                         = 0
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   nstdisreout                    = 100
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   orire-fc                       = 0
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   orire-tau                      = 0
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   nstorireout                    = 100
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   free-energy                    = no
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   cos-acceleration               = 0
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   deform (3x3):
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      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   simulated-tempering            = false
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   swapcoords                     = no
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   userint1                       = 0
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   userint2                       = 0
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   userint3                       = 0
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   userint4                       = 0
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   userreal1                      = 0
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   userreal2                      = 0
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   userreal3                      = 0
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   userreal4                      = 0
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   applied-forces:
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     electric-field:
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       x:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       y:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       z:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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grpopts:
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   nrdf:      443877
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   ref-t:           0
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   tau-t:           0
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annealing:          No
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annealing-npoints:           0
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   acc:	           0           0           0
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   nfreeze:           N           N           N
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   energygrp-flags[  0]: 0
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Using SIMD all-vs-all kernels.
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NOTE: GROMACS was compiled without OpenMP and (thread-)MPI support, can only use a single CPU core
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Pinning threads with an auto-selected logical core stride of 1
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Your simulation settings would have triggered the efficient all-vs-all
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kernels in GROMACS 4.5, but these have not been implemented in GROMACS
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4.6 and 5.x. If performance is important, please use GROMACS 4.5.7
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or try cutoff-scheme = Verlet.
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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: 600.000
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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: 1e+18   Coulomb: 1e+18   LJ: 1e+18
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Generated table with 500 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 500 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 500 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Initiating Steepest Descents
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Started Steepest Descents on rank 0 Wed Apr 24 12:47:04 2019
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Steepest Descents:
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   Tolerance (Fmax)   =  1.00000e+03
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   Number of steps    =        10000
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Grid: 20 x 20 x 20 cells
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-------------------------------------------------------
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Program:     gmx mdrun, version 2018.6
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Source file: src/gromacs/utility/smalloc.cpp (line 226)
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Fatal error:
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Not enough memory. Failed to realloc -8589934592 bytes for nlist->jjnr,
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nlist->jjnr=3eb9a010
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(called from file
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/sw/apps/gromacs/2018.6/rackham_build/gromacs-2018.6/src/gromacs/mdlib/ns.cpp,
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line 477)
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For more information and tips for troubleshooting, please check the GROMACS
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website at http://www.gromacs.org/Documentation/Errors
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-------------------------------------------------------