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0519-updategroups-1node.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    
6
 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
17

    
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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:   13456
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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 1 node with total 28 cores, 28 logical cores
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Hardware detected on host r2c10cn4 (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
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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
98
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
115
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
148
   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
153
   comm-mode                      = Linear
154
   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 28 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 24 particle-particle and 4 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 4 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 24 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 3 x 2, separate PME ranks 4
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PME domain decomposition: 4 x 1 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 4.41 nm Z 6.01 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)  3.628 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 0.30 Z 0.22
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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
396

    
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Using 28 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 ++++
408
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
409
A smooth particle mesh Ewald method
410
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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431
Using SIMD 4x8 nonbonded short-range kernels
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Using a dual 4x8 pair-list setup updated with dynamic pruning:
434
  outer list: updated every 80 steps, buffer 0.126 nm, rlist 1.326 nm
435
  inner list: updated every 13 steps, buffer 0.002 nm, rlist 1.202 nm
436
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
437
  outer list: updated every 80 steps, buffer 0.275 nm, rlist 1.475 nm
438
  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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443
Will apply potential COM pulling
444
with 1 pull coordinate and 2 groups
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Pull group 1:     1 atoms, mass    13.019
446
Pull group 2:     2 atoms, mass    26.018
447

    
448
Initializing Parallel LINear Constraint Solver
449

    
450
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
451
B. Hess
452
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
453
J. Chem. Theory Comput. 4 (2008) pp. 116-122
454
-------- -------- --- Thank You --- -------- --------
455

    
456
The number of constraints is 1073
457
There are constraints between atoms in different decomposition domains,
458
will communicate selected coordinates each lincs iteration
459

    
460
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
461
S. Miyamoto and P. A. Kollman
462
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
463
Water Models
464
J. Comp. Chem. 13 (1992) pp. 952-962
465
-------- -------- --- Thank You --- -------- --------
466

    
467

    
468
Linking all bonded interactions to atoms
469

    
470

    
471
The -noconfout functionality is deprecated, and may be removed in a future version.
472

    
473
Intra-simulation communication will occur every 20 steps.
474
Center of mass motion removal mode is Linear
475
We have the following groups for center of mass motion removal:
476
  0:  rest
477

    
478
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
479
G. Bussi, D. Donadio and M. Parrinello
480
Canonical sampling through velocity rescaling
481
J. Chem. Phys. 126 (2007) pp. 014101
482
-------- -------- --- Thank You --- -------- --------
483

    
484
There are: 224238 Atoms
485
Atom distribution over 24 domains: av 9343 stddev 159 min 8986 max 9487
486

    
487
Started mdrun on rank 0 Mon Apr 29 17:41:50 2019
488

    
489
           Step           Time
490
              0        0.00000
491

    
492
   Energies (kJ/mol)
493
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
494
    5.09961e+03    7.77425e+03    4.85656e+03    2.47900e+03   -1.61705e+02
495
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
496
    6.64263e+04    5.11422e+05   -1.65591e+04   -3.68724e+06    1.05263e+04
497
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
498
    6.82855e-14   -3.09538e+06    9.65238e+03   -3.08573e+06   -3.08550e+06
499
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
500
    5.13609e+00   -1.19286e+02   -1.38955e+03    2.44768e-06
501

    
502

    
503
DD  step 79 load imb.: force  1.0%  pme mesh/force 0.641
504

    
505
DD  step 49999 load imb.: force  0.1%  pme mesh/force 0.636
506
           Step           Time
507
          50000      100.00000
508

    
509
   Energies (kJ/mol)
510
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
511
    5.07309e+03    7.88547e+03    4.77681e+03    2.53831e+03   -1.25494e+02
512
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
513
    6.62515e+04    5.14346e+05   -1.65502e+04   -3.69187e+06    1.06637e+04
514
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
515
    2.05921e+00   -3.09701e+06    5.65433e+05   -2.53158e+06   -3.10370e+06
516
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
517
    3.00870e+02   -1.19158e+02    6.88380e+00    2.90667e-06
518

    
519
Writing checkpoint, step 51600 at Mon Apr 29 17:56:51 2019
520

    
521

    
522

    
523
DD  step 99999 load imb.: force  0.1%  pme mesh/force 0.629
524
           Step           Time
525
         100000      200.00000
526

    
527
   Energies (kJ/mol)
528
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
529
    4.83947e+03    7.76333e+03    5.02919e+03    2.57352e+03   -2.01676e+02
530
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
531
    6.63908e+04    5.11349e+05   -1.65637e+04   -3.68742e+06    1.05885e+04
532
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
533
    8.22999e+00   -3.09564e+06    5.64535e+05   -2.53111e+06   -3.10244e+06
534
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
535
    3.00392e+02   -1.19353e+02   -1.15791e+01    2.85825e-06
536

    
537
Writing checkpoint, step 103200 at Mon Apr 29 18:11:51 2019
538

    
539

    
540

    
541
DD  step 149999 load imb.: force  0.1%  pme mesh/force 0.629
542
           Step           Time
543
         150000      300.00000
544

    
545
   Energies (kJ/mol)
546
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
547
    4.73493e+03    7.51411e+03    4.79377e+03    2.62355e+03   -1.61440e+02
548
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
549
    6.65032e+04    5.13268e+05   -1.65593e+04   -3.69267e+06    1.06059e+04
550
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
551
    1.06595e+01   -3.09934e+06    5.61731e+05   -2.53761e+06   -3.10114e+06
552
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
553
    2.98900e+02   -1.19289e+02    3.20921e+01    2.72740e-06
554

    
555
Writing checkpoint, step 154720 at Mon Apr 29 18:26:50 2019
556

    
557

    
558

    
559
DD  step 199999 load imb.: force  0.1%  pme mesh/force 0.629
560
           Step           Time
561
         200000      400.00000
562

    
563
   Energies (kJ/mol)
564
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
565
    4.72977e+03    7.77913e+03    4.97781e+03    2.64590e+03   -1.86805e+02
566
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
567
    6.65539e+04    5.12121e+05   -1.65476e+04   -3.68970e+06    1.06055e+04
568
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
569
    1.13379e+01   -3.09701e+06    5.63238e+05   -2.53377e+06   -3.09980e+06
570
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
571
    2.99702e+02   -1.19120e+02    7.92175e-01    2.82831e-06
572

    
573

    
574
Step 204240: Run time exceeded 0.990 hours, will terminate the run within 80 steps
575
           Step           Time
576
         204320      408.64000
577

    
578
   Energies (kJ/mol)
579
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
580
    4.92980e+03    7.61687e+03    4.96679e+03    2.53375e+03   -3.05528e+02
581
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
582
    6.64921e+04    5.13116e+05   -1.65538e+04   -3.69267e+06    1.05618e+04
583
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
584
    1.42167e+01   -3.09930e+06    5.64881e+05   -2.53442e+06   -3.09968e+06
585
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
586
    3.00577e+02   -1.19210e+02   -2.00279e+01    2.79905e-06
587

    
588
	<======  ###############  ==>
589
	<====  A V E R A G E S  ====>
590
	<==  ###############  ======>
591

    
592
	Statistics over 204321 steps using 2044 frames
593

    
594
   Energies (kJ/mol)
595
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
596
    4.92036e+03    7.68631e+03    4.89835e+03    2.55049e+03   -1.99119e+02
597
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
598
    6.64616e+04    5.13012e+05   -1.65583e+04   -3.69162e+06    1.06089e+04
599
   COM Pull En.      Potential    Kinetic En.   Total Energy  Conserved En.
600
    6.17256e+00   -3.09823e+06    5.63468e+05   -2.53476e+06   -3.10236e+06
601
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
602
    2.99824e+02   -1.19275e+02    2.23477e-01    0.00000e+00
603

    
604
          Box-X          Box-Y          Box-Z
605
    1.45131e+01    1.32260e+01    1.20181e+01
606

    
607
   Total Virial (kJ/mol)
608
    1.87654e+05    7.26374e+01    1.12804e+02
609
    6.93176e+01    1.87756e+05   -2.64689e+01
610
    1.08856e+02   -2.62935e+01    1.88012e+05
611

    
612
   Pressure (bar)
613
    2.26382e+00   -1.00341e+00   -1.46889e+00
614
   -9.55656e-01    1.18775e+00    2.94279e-01
615
   -1.41206e+00    2.91779e-01   -2.78115e+00
616

    
617
T-protein_and_gpfT-water_and_ions
618
    2.99917e+02    2.99822e+02
619

    
620

    
621
	M E G A - F L O P S   A C C O U N T I N G
622

    
623
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
624
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
625
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
626
 V&F=Potential and force  V=Potential only  F=Force only
627

    
628
 Computing:                               M-Number         M-Flops  % Flops
629
-----------------------------------------------------------------------------
630
 Pair Search distance check          314388.467106     2829496.204     0.1
631
 NxN Ewald Elec. + LJ [F]          20746621.748032  1369277035.370    51.0
632
 NxN Ewald Elec. + LJ [V&F]          209746.607680    22442887.022     0.8
633
 NxN LJ [F]                           27932.911872      921786.092     0.0
634
 NxN LJ [V&F]                           282.407584       12143.526     0.0
635
 NxN Ewald Elec. [F]               19665342.884864  1199585915.977    44.6
636
 NxN Ewald Elec. [V&F]               198815.960544    16700540.686     0.6
637
 1,4 nonbonded interactions            1499.511819      134956.064     0.0
638
 Calc Weights                        137449.597194     4948185.499     0.2
639
 Spread Q Bspline                   2932258.073472     5864516.147     0.2
640
 Gather F Bspline                   2932258.073472    17593548.441     0.7
641
 3D-FFT                             5087717.535810    40701740.286     1.5
642
 Solve PME                             1647.644544      105449.251     0.0
643
 Reset In Box                           572.703852        1718.112     0.0
644
 CG-CoM                                 572.928090        1718.784     0.0
645
 Bonds                                  755.579058       44579.164     0.0
646
 Angles                                1436.172309      241276.948     0.0
647
 Propers                                670.377201      153516.379     0.0
648
 Impropers                              525.922254      109391.829     0.0
649
 Virial                                2302.074006       41437.332     0.0
650
 Stop-CM                                458.342472        4583.425     0.0
651
 P-Coupling                            2291.039646       13746.238     0.0
652
 Calc-Ekin                             4582.079292      123716.141     0.0
653
 Lincs                                  229.643530       13778.612     0.0
654
 Lincs-Mat                              393.726732        1574.907     0.0
655
 Constraint-V                         48026.130248      384209.042     0.0
656
 Constraint-Vir                        2390.046330       57361.112     0.0
657
 Settle                               15855.614396     5121363.450     0.2
658
-----------------------------------------------------------------------------
659
 Total                                              2687432172.038   100.0
660
-----------------------------------------------------------------------------
661

    
662

    
663
    D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S
664

    
665
 av. #atoms communicated per step for force:  2 x 246696.7
666
 av. #atoms communicated per step for LINCS:  2 x 13446.5
667

    
668

    
669
Dynamic load balancing report:
670
 DLB was off during the run due to low measured imbalance.
671
 Average load imbalance: 0.1%.
672
 The balanceable part of the MD step is 94%, load imbalance is computed from this.
673
 Part of the total run time spent waiting due to load imbalance: 0.1%.
674
 Average PME mesh/force load: 0.626
675
 Part of the total run time spent waiting due to PP/PME imbalance: 5.0 %
676

    
677
NOTE: 5.0 % performance was lost because the PME ranks
678
      had less work to do than the PP ranks.
679
      You might want to decrease the number of PME ranks
680
      or decrease the cut-off and the grid spacing.
681

    
682

    
683
     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
684

    
685
On 24 MPI ranks doing PP, and
686
on 4 MPI ranks doing PME
687

    
688
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
689
                     Ranks Threads  Count      (s)         total sum    %
690
-----------------------------------------------------------------------------
691
 Domain decomp.        24    1       2554      16.469        948.609   0.4
692
 DD comm. load         24    1         30       0.000          0.018   0.0
693
 Send X to PME         24    1     204321      25.447       1465.761   0.6
694
 Neighbor search       24    1       2555      51.089       2942.769   1.2
695
 Comm. coord.          24    1     201766      37.600       2165.797   0.9
696
 Force                 24    1     204321    3146.792     181257.095  75.6
697
 Wait + Comm. F        24    1     204321      23.666       1363.155   0.6
698
 PME mesh *             4    1     204321    2080.840      19976.273   8.3
699
 PME wait for PP *                           1485.242      14258.471   5.9
700
 Wait + Recv. PME F    24    1     204321      17.680       1018.379   0.4
701
 NB X/F buffer ops.    24    1     607853      28.278       1628.805   0.7
702
 COM pull force        24    1     204321     153.254       8827.496   3.7
703
 Write traj.           24    1          8       0.032          1.829   0.0
704
 Update                24    1     204321      23.097       1330.399   0.6
705
 Constraints           24    1     204321      38.073       2193.007   0.9
706
 Comm. energies        24    1      10217       0.472         27.187   0.0
707
 Rest                                           4.167        240.005   0.1
708
-----------------------------------------------------------------------------
709
 Total                                       3566.114     239645.361 100.0
710
-----------------------------------------------------------------------------
711
(*) Note that with separate PME ranks, the walltime column actually sums to
712
    twice the total reported, but the cycle count total and % are correct.
713
-----------------------------------------------------------------------------
714
 Breakdown of PME mesh computation
715
-----------------------------------------------------------------------------
716
 PME redist. X/F        4    1     408642     166.921       1602.456   0.7
717
 PME spread             4    1     204321     789.959       7583.685   3.2
718
 PME gather             4    1     204321     481.080       4618.417   1.9
719
 PME 3D-FFT             4    1     408642     535.328       5139.201   2.1
720
 PME 3D-FFT Comm.       4    1     408642      58.858        565.038   0.2
721
 PME solve Elec         4    1     204321      47.900        459.842   0.2
722
-----------------------------------------------------------------------------
723

    
724
               Core t (s)   Wall t (s)        (%)
725
       Time:    99851.151     3566.114     2800.0
726
                         59:26
727
                 (ns/day)    (hour/ns)
728
Performance:        9.901        2.424
729
Finished mdrun on rank 0 Mon Apr 29 18:41:16 2019
730