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0519-updategroups-4nodes.log

Stefan Becuwe, 04/30/2019 08:16 AM

 
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                      :-) GROMACS - gmx mdrun, 2019.1 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
5
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
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 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
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  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
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  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
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    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
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  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
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    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
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    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
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   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
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 Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2018, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
25
under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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GROMACS:      gmx mdrun, version 2019.1
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Executable:   /apps/broadwell/centos7/GROMACS/2019.1-intel-2018b-UArecipe/bin/gmx_mpi
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Data prefix:  /apps/broadwell/centos7/GROMACS/2019.1-intel-2018b-UArecipe
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Working dir:  /scratch/gromacs-2019/2018u3-2019.2
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Process ID:   7244
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Command line:
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  gmx_mpi mdrun -ntomp 1 -s 0519.tpr -o /scratch/gromacs-2019/2018u3-2019.2/0519.trr -x /scratch/gromacs-2019/2018u3-2019.2/0519.xtc -cpo /scratch/gromacs-2019/2018u3-2019.2/0519.cpt -c /scratch/gromacs-2019/2018u3-2019.2/0519.gro -e /scratch/gromacs-2019/2018u3-2019.2/0519.edr -dhdl /scratch/gromacs-2019/2018u3-2019.2/0519.xvg -g /scratch/gromacs-2019/2018u3-2019.2/0519.log -px /scratch/gromacs-2019/2018u3-2019.2/0519.x.xvg -pf /scratch/gromacs-2019/2018u3-2019.2/0519.f.xvg -noconfout -rcon 0.7 -pin on -dds 0.9 -dlb auto -maxh 1
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GROMACS version:    2019.1
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Precision:          single
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Memory model:       64 bit
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MPI library:        MPI
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support:        disabled
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SIMD instructions:  AVX2_256
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FFT library:        Intel MKL
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      hwloc-1.11.8
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Tracing support:    disabled
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C compiler:         /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicc Intel 18.0.3.20180410
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C compiler flags:    -march=core-avx2   -mkl=sequential  -std=gnu99  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits  
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C++ compiler:       /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicpc Intel 18.0.3.20180410
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C++ compiler flags:  -march=core-avx2   -mkl=sequential  -std=c++11   -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits  
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Running on 4 nodes with total 112 cores, 112 logical cores
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  Cores per node:           28
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  Logical cores per node:   28
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Hardware detected on host r3c07cn2 (the node of MPI rank 0):
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  CPU info:
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    Vendor: Intel
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    Brand:  Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
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    Family: 6   Model: 79   Stepping: 1
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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  Hardware topology: Full, with devices
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    Sockets, cores, and logical processors:
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      Socket  0: [   0] [   1] [   2] [   3] [   4] [   5] [   6] [   7] [   8] [   9] [  10] [  11] [  12] [  13]
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      Socket  1: [  14] [  15] [  16] [  17] [  18] [  19] [  20] [  21] [  22] [  23] [  24] [  25] [  26] [  27]
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    Numa nodes:
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      Node  0 (68600541184 bytes mem):   0   1   2   3   4   5   6   7   8   9  10  11  12  13
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      Node  1 (68719476736 bytes mem):  14  15  16  17  18  19  20  21  22  23  24  25  26  27
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      Latency:
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               0     1
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         0  1.00  2.10
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         1  2.10  1.00
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    Caches:
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      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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      L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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      L3: 36700160 bytes, linesize 64 bytes, assoc. 20, shared 14 ways
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    PCI devices:
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      0000:01:00.0  Id: 8086:1521  Class: 0x0200  Numa: 0
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      0000:01:00.1  Id: 8086:1521  Class: 0x0200  Numa: 0
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      0000:02:00.0  Id: 15b3:1013  Class: 0x0207  Numa: 0
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      0000:00:11.4  Id: 8086:8d62  Class: 0x0106  Numa: 0
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      0000:07:00.0  Id: 1a03:2000  Class: 0x0300  Numa: 0
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      0000:00:1f.2  Id: 8086:8d02  Class: 0x0106  Numa: 0
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
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Lindahl
91
GROMACS: High performance molecular simulations through multi-level
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parallelism from laptops to supercomputers
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SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
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GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
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GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
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https://doi.org/10.5281/zenodo.2564764
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-------- -------- --- Thank You --- -------- --------
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Input Parameters:
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   integrator                     = md
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   tinit                          = 0
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   dt                             = 0.002
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   nsteps                         = 500000
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   init-step                      = 0
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   simulation-part                = 1
155
   comm-mode                      = Linear
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   nstcomm                        = 100
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   bd-fric                        = 0
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   ld-seed                        = -1437393019
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   emtol                          = 10
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   emstep                         = 0.01
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   niter                          = 20
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   fcstep                         = 0
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   nstcgsteep                     = 1000
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   nbfgscorr                      = 10
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   rtpi                           = 0.05
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   nstxout                        = 0
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   nstvout                        = 0
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   nstfout                        = 0
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   nstlog                         = 50000
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   nstcalcenergy                  = 100
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   nstenergy                      = 50000
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   nstxout-compressed             = 50000
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
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   nstlist                        = 20
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   ns-type                        = Grid
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   pbc                            = xyz
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   periodic-molecules             = false
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   verlet-buffer-tolerance        = 0.005
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   rlist                          = 1.223
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   coulombtype                    = PME
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   coulomb-modifier               = Potential-shift
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   rcoulomb-switch                = 0
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   rcoulomb                       = 1.2
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   epsilon-r                      = 1
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   epsilon-rf                     = inf
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   vdw-type                       = Cut-off
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   vdw-modifier                   = Potential-shift
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   rvdw-switch                    = 1
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   rvdw                           = 1.2
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   DispCorr                       = EnerPres
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   table-extension                = 1
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   fourierspacing                 = 0.16
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   fourier-nx                     = 96
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   fourier-ny                     = 84
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   fourier-nz                     = 80
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   pme-order                      = 4
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   ewald-rtol                     = 1e-05
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   ewald-rtol-lj                  = 0.001
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   lj-pme-comb-rule               = Geometric
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   ewald-geometry                 = 0
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   epsilon-surface                = 0
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   tcoupl                         = V-rescale
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   nsttcouple                     = 20
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = Berendsen
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   pcoupltype                     = Isotropic
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   nstpcouple                     = 20
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   tau-p                          = 2
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   compressibility (3x3):
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      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
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   ref-p (3x3):
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      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
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   refcoord-scaling               = COM
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   posres-com (3):
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      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = false
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = true
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 4
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   lincs-iter                     = 1
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   lincs-warnangle                = 30
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   nwall                          = 0
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   wall-type                      = 9-3
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   wall-r-linpot                  = -1
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   wall-atomtype[0]               = -1
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   wall-atomtype[1]               = -1
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   wall-density[0]                = 0
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   wall-density[1]                = 0
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   wall-ewald-zfac                = 3
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   pull                           = true
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   pull-cylinder-r                = 1.5
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   pull-constr-tol                = 1e-06
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   pull-print-COM                 = true
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   pull-print-ref-value           = true
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   pull-print-components          = true
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   pull-nstxout                   = 50000
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   pull-nstfout                   = 50000
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   pull-pbc-ref-prev-step-com     = false
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   pull-xout-average              = false
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   pull-fout-average              = false
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   pull-ngroups                   = 3
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   pull-group 0:
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     atom: not available
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     weight: not available
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     pbcatom                        = -1
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   pull-group 1:
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     atom (1):
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        atom[0]=1442
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     weight: not available
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     pbcatom                        = -1
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   pull-group 2:
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     atom (2):
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        atom[0]=4641
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        atom[1]=4643
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     weight: not available
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     pbcatom                        = 4641
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   pull-ncoords                   = 1
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   pull-coord 0:
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   type                           = umbrella
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   geometry                       = distance
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   group[0]                       = 1
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   group[1]                       = 2
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   dim (3):
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      dim[0]=1
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      dim[1]=1
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      dim[2]=1
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   origin (3):
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      origin[0]= 0.00000e+00
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      origin[1]= 0.00000e+00
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      origin[2]= 0.00000e+00
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   vec (3):
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      vec[0]= 0.00000e+00
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      vec[1]= 0.00000e+00
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      vec[2]= 0.00000e+00
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   start                          = true
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   init                           = 0.518654
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   rate                           = 0
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   k                              = 1000
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   kB                             = 1000
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   awh                            = false
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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = No
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   disre-weighting                = Conservative
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   disre-mixed                    = false
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   dr-fc                          = 1000
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   dr-tau                         = 0
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   nstdisreout                    = 100
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   orire-fc                       = 0
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   orire-tau                      = 0
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   nstorireout                    = 100
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   free-energy                    = no
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   cos-acceleration               = 0
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   deform (3x3):
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      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   simulated-tempering            = false
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   swapcoords                     = no
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   userint1                       = 0
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   userint2                       = 0
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   userint3                       = 0
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   userint4                       = 0
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   userreal1                      = 0
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   userreal2                      = 0
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   userreal3                      = 0
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   userreal4                      = 0
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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:     12909.9      439152
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   ref-t:         300         300
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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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Changing nstlist from 20 to 80, rlist from 1.223 to 1.326
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Initializing Domain Decomposition on 112 ranks
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Dynamic load balancing: locked
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Minimum cell size due to atom displacement: 0.514 nm
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Initial maximum distances in bonded interactions:
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    two-body bonded interactions: 0.443 nm, LJ-14, atoms 1990 2780
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  multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1990 2780
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Minimum cell size due to bonded interactions: 0.487 nm
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User supplied maximum distance required for P-LINCS: 0.700 nm
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Guess for relative PME load: 0.13
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Will use 96 particle-particle and 16 PME only ranks
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This is a guess, check the performance at the end of the log file
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Using 16 separate PME ranks, as guessed by mdrun
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Scaling the initial minimum size with 1/0.9 (option -dds) = 1.11111
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Optimizing the DD grid for 96 cells with a minimum initial size of 0.778 nm
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The maximum allowed number of cells is: X 18 Y 17 Z 15
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Domain decomposition grid 4 x 4 x 6, separate PME ranks 16
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PME domain decomposition: 4 x 4 x 1
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Interleaving PP and PME ranks
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This rank does only particle-particle work.
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Domain decomposition rank 0, coordinates 0 0 0
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The initial number of communication pulses is: X 1 Y 1 Z 1
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The initial domain decomposition cell size is: X 3.63 nm Y 3.31 nm Z 2.00 nm
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The maximum allowed distance for atoms involved in interactions is:
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                 non-bonded interactions           1.326 nm
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(the following are initial values, they could change due to box deformation)
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            two-body bonded interactions  (-rdd)   1.326 nm
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          multi-body bonded interactions  (-rdd)   1.326 nm
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  atoms separated by up to 5 constraints  (-rcon)  2.003 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 1 Y 1 Z 1
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The minimum size for domain decomposition cells is 1.326 nm
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The requested allowed shrink of DD cells (option -dds) is: 0.90
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The allowed shrink of domain decomposition cells is: X 0.37 Y 0.40 Z 0.66
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The maximum allowed distance for atoms involved in interactions is:
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                 non-bonded interactions           1.326 nm
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            two-body bonded interactions  (-rdd)   1.326 nm
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          multi-body bonded interactions  (-rdd)   1.326 nm
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  atoms separated by up to 5 constraints  (-rcon)  1.326 nm
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Using two step summing over 4 groups of on average 24.0 ranks
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Using 112 MPI processes
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Using 1 OpenMP thread per MPI process
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Overriding thread affinity set outside gmx mdrun
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Pinning threads with an auto-selected logical core stride of 1
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System total charge: -0.000
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Will do PME sum in reciprocal space for electrostatic interactions.
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
412
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
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A smooth particle mesh Ewald method
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J. Chem. Phys. 103 (1995) pp. 8577-8592
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-------- -------- --- Thank You --- -------- --------
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Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
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Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -8.333e-06
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Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
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Long Range LJ corr.: <C6> 3.1361e-04
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Generated table with 1163 data points for Ewald.
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Tabscale = 500 points/nm
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Generated table with 1163 data points for LJ6.
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Tabscale = 500 points/nm
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Generated table with 1163 data points for LJ12.
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Tabscale = 500 points/nm
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Generated table with 1163 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1163 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1163 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Using SIMD 4x8 nonbonded short-range kernels
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Using a dual 4x8 pair-list setup updated with dynamic pruning:
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  outer list: updated every 80 steps, buffer 0.126 nm, rlist 1.326 nm
439
  inner list: updated every 13 steps, buffer 0.002 nm, rlist 1.202 nm
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At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
441
  outer list: updated every 80 steps, buffer 0.275 nm, rlist 1.475 nm
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  inner list: updated every 13 steps, buffer 0.052 nm, rlist 1.252 nm
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Using full Lennard-Jones parameter combination matrix
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Will apply potential COM pulling
448
with 1 pull coordinate and 2 groups
449
Pull group 1:     1 atoms, mass    13.019
450
Pull group 2:     2 atoms, mass    26.018
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Will use a sub-communicator for pull communication
452

    
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Initializing Parallel LINear Constraint Solver
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455
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
456
B. Hess
457
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
458
J. Chem. Theory Comput. 4 (2008) pp. 116-122
459
-------- -------- --- Thank You --- -------- --------
460

    
461
The number of constraints is 1073
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There are constraints between atoms in different decomposition domains,
463
will communicate selected coordinates each lincs iteration
464

    
465
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
466
S. Miyamoto and P. A. Kollman
467
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
468
Water Models
469
J. Comp. Chem. 13 (1992) pp. 952-962
470
-------- -------- --- Thank You --- -------- --------
471

    
472

    
473
Linking all bonded interactions to atoms
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475

    
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The -noconfout functionality is deprecated, and may be removed in a future version.
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Intra-simulation communication will occur every 20 steps.
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Center of mass motion removal mode is Linear
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We have the following groups for center of mass motion removal:
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  0:  rest
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++++ 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: 224238 Atoms
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Atom distribution over 96 domains: av 2335 stddev 86 min 2090 max 2430
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Started mdrun on rank 0 Mon Apr 29 22:52:24 2019
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           Step           Time
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              0        0.00000
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   Energies (kJ/mol)
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        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
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    5.09960e+03    7.77425e+03    4.85656e+03    2.47900e+03   -1.61705e+02
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     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
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    6.64263e+04    5.11422e+05   -1.65591e+04   -3.68724e+06    1.05264e+04
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   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
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    6.82855e-14   -3.09538e+06    9.65238e+03   -3.08573e+06   -3.08550e+06
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    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
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    5.13609e+00   -1.19286e+02   -1.38954e+03    2.44671e-06
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