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test-2.log

mdrun log file for broken run - Eiso AB, 05/15/2019 09:02 AM

 
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Log file opened on Wed May 15 00:58:01 2019
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Host: zb-svr-02.zobio.local  pid: 6820  rank ID: 0  number of ranks:  1
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                    :-) GROMACS - gmx mdrun, 2019-beta1 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
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    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  
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  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   
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 Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    
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  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  
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  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   
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    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  
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   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen 
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 Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2017, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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-beta1
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Executable:   /usr/local/gromacs/bin/gmx
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Data prefix:  /usr/local/gromacs
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Working dir:  /home/eiso/gmx-test/ORIG-ZB2
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Command line:
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  gmx mdrun -v -deffnm test -c test.pdb
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GROMACS version:    2019-beta1
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Precision:          single
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Memory model:       64 bit
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MPI library:        thread_mpi
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support:        disabled
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SIMD instructions:  AVX2_256
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FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128
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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:         /usr/bin/cc GNU 4.8.5
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C compiler flags:    -mavx2 -mfma     -O2 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /usr/bin/c++ GNU 4.8.5
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C++ compiler flags:  -mavx2 -mfma    -std=c++11   -O2 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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Running on 1 node with total 32 cores, 32 logical cores
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Hardware detected:
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  CPU info:
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    Vendor: Intel
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    Brand:  Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz
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    Family: 6   Model: 63   Stepping: 2
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma intel lahf mmx msr nonstop_tsc pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp 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] [  14] [  15]
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      Socket  1: [  16] [  17] [  18] [  19] [  20] [  21] [  22] [  23] [  24] [  25] [  26] [  27] [  28] [  29] [  30] [  31]
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    Numa nodes:
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      Node  0 (26843013120 bytes mem):   0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
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      Node  1 (26843545600 bytes mem):  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30  31
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      Latency:
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               0     1
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         0  1.00  2.00
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         1  2.00  1.00
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    Caches:
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      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 16 ways
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      L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 16 ways
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      L3: 31457280 bytes, linesize 64 bytes, assoc. 20, shared 16 ways
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    PCI devices:
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      0000:00:07.1  Id: 8086:7111  Class: 0x0101  Numa: -1
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      0000:00:0f.0  Id: 15ad:0405  Class: 0x0300  Numa: -1
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      0000:00:10.0  Id: 1000:0030  Class: 0x0100  Numa: -1
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      0000:03:00.0  Id: 15ad:07b0  Class: 0x0200  Numa: -1
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
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Lindahl
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GROMACS: High performance molecular simulations through multi-level
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parallelism from laptops to supercomputers
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SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
95
GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
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GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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Input Parameters:
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   integrator                     = md
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   tinit                          = 0
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   dt                             = 0.002
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   nsteps                         = 50000
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   init-step                      = 0
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   simulation-part                = 1
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   comm-mode                      = Linear
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   nstcomm                        = 100
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   bd-fric                        = 0
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   ld-seed                        = 1993
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   emtol                          = 100
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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                         = 5000
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   nstcalcenergy                  = 100
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   nstenergy                      = 0
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   nstxout-compressed             = 500
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
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   nstlist                        = 10
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   ns-type                        = Grid
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   pbc                            = xyz
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   periodic-molecules             = false
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   verlet-buffer-tolerance        = 0.005
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   rlist                          = 0.969
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   coulombtype                    = Reaction-Field
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   coulomb-modifier               = Potential-shift
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   rcoulomb-switch                = 0
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   rcoulomb                       = 0.9
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   epsilon-r                      = 1
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   epsilon-rf                     = inf
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   vdw-type                       = Cut-off
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   vdw-modifier                   = Potential-shift
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   rvdw-switch                    = 0
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   rvdw                           = 0.9
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.12
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   fourier-nx                     = 28
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   fourier-ny                     = 28
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   fourier-nz                     = 28
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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                     = 10
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = No
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   pcoupltype                     = Isotropic
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   nstpcouple                     = -1
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   tau-p                          = 2
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   compressibility (3x3):
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      compressibility[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   ref-p (3x3):
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      ref-p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   refcoord-scaling               = No
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   posres-com (3):
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      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = false
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = false
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 4
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   lincs-iter                     = 1
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   lincs-warnangle                = 30
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   nwall                          = 0
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   wall-type                      = 9-3
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   wall-r-linpot                  = -1
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   wall-atomtype[0]               = -1
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   wall-atomtype[1]               = -1
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   wall-density[0]                = 0
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   wall-density[1]                = 0
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   wall-ewald-zfac                = 3
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   pull                           = false
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   awh                            = false
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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = Simple
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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
253
   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}
258
   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:
276
         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:
281
         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:        2397
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   ref-t:         298
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   tau-t:         0.5
289
annealing:          No
290
annealing-npoints:           0
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   acc:	           0           0           0
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   nfreeze:           N           N           N
293
   energygrp-flags[  0]: 0
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Changing nstlist from 10 to 20, rlist from 0.969 to 1.075
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Initializing Domain Decomposition on 12 ranks
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Dynamic load balancing: locked
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The combination of rlist and box size prohibits the use of update groups
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Minimum cell size due to atom displacement: 0.282 nm
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Initial maximum distances in bonded interactions:
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    two-body bonded interactions: 0.164 nm, Exclusion, atoms 1124 1125
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Minimum cell size due to bonded interactions: 0.000 nm
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Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
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Optimizing the DD grid for 12 cells with a minimum initial size of 0.352 nm
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The maximum allowed number of cells is: X 6 Y 6 Z 6
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Domain decomposition grid 4 x 3 x 1, separate PME ranks 0
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Domain decomposition rank 0, coordinates 0 0 0
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The initial number of communication pulses is: X 2 Y 2
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The initial domain decomposition cell size is: X 0.57 nm Y 0.76 nm
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The maximum allowed distance for atoms involved in interactions is:
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                 non-bonded interactions           1.075 nm
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            two-body bonded interactions  (-rdd)   1.075 nm
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          multi-body bonded interactions  (-rdd)   0.573 nm
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  atoms separated by up to 5 constraints  (-rcon)  0.573 nm
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When dynamic load balancing gets turned on, these settings will change to:
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The maximum number of communication pulses is: X 3 Y 2
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The minimum size for domain decomposition cells is 0.358 nm
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The requested allowed shrink of DD cells (option -dds) is: 0.80
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The allowed shrink of domain decomposition cells is: X 0.62 Y 0.70
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The maximum allowed distance for atoms involved in interactions is:
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                 non-bonded interactions           1.075 nm
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            two-body bonded interactions  (-rdd)   1.075 nm
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          multi-body bonded interactions  (-rdd)   0.358 nm
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  atoms separated by up to 5 constraints  (-rcon)  0.358 nm
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Using 12 MPI threads
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Using 2 OpenMP threads per tMPI thread
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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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Reaction-Field:
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epsRF = 0, rc = 0.9, krf = 0.685871, crf = 1.66667, epsfac = 138.935
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The electrostatics potential has its minimum at r = 0.9
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Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00
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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 20 steps, buffer 0.175 nm, rlist 1.075 nm
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  inner list: updated every  4 steps, buffer 0.014 nm, rlist 0.914 nm
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At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
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  outer list: updated every 20 steps, buffer 0.224 nm, rlist 1.124 nm
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  inner list: updated every  4 steps, buffer 0.023 nm, rlist 0.923 nm
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Using geometric Lennard-Jones combination rule
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Removing pbc first time
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
355
S. Miyamoto and P. A. Kollman
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SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
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Water Models
358
J. Comp. Chem. 13 (1992) pp. 952-962
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-------- -------- --- Thank You --- -------- --------
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Linking all bonded interactions to atoms
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Intra-simulation communication will occur every 10 steps.
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Center of mass motion removal mode is 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 ++++
371
G. Bussi, D. Donadio and M. Parrinello
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Canonical sampling through velocity rescaling
373
J. Chem. Phys. 126 (2007) pp. 014101
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-------- -------- --- Thank You --- -------- --------
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There are: 1200 Atoms
377
Atom distribution over 12 domains: av 100 stddev 4 min 94 max 107
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Constraining the starting coordinates (step 0)
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Constraining the coordinates at t0-dt (step 0)
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RMS relative constraint deviation after constraining: 0.00e+00
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Initial temperature: 295.783 K
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Started mdrun on rank 0 Wed May 15 00:58:01 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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        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
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    3.94214e+03   -2.25672e+04   -1.86251e+04    2.99270e+03   -1.56324e+04
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  Conserved En.    Temperature Pressure (bar)
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   -1.56324e+04    3.00325e+02    5.75158e+02
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DD  step 19 load imb.: force 17.0%
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step 40 Turning on dynamic load balancing, because the performance loss due to load imbalance is 2.6 %.
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DD  step 4999  vol min/aver 0.745  load imb.: force  8.4%
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           Step           Time
403
           5000       10.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
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    3.85531e+03   -2.25524e+04   -1.86971e+04    2.91752e+03   -1.57796e+04
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  Conserved En.    Temperature Pressure (bar)
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   -1.56114e+04    2.92781e+02   -2.02508e+02
410

    
411

    
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DD  step 9999  vol min/aver 0.679  load imb.: force  8.7%
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           Step           Time
414
          10000       20.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
418
    3.81238e+03   -2.24239e+04   -1.86116e+04    2.93995e+03   -1.56716e+04
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  Conserved En.    Temperature Pressure (bar)
420
   -1.55885e+04    2.95031e+02    2.35051e+02
421

    
422

    
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DD  step 14999  vol min/aver 0.681  load imb.: force 12.2%
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           Step           Time
425
          15000       30.00000
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427
   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
429
    3.94682e+03   -2.26588e+04   -1.87120e+04    2.92032e+03   -1.57917e+04
430
  Conserved En.    Temperature Pressure (bar)
431
   -1.55663e+04    2.93061e+02    4.64213e+02
432

    
433

    
434
DD  step 19999  vol min/aver 0.656  load imb.: force  9.5%
435
           Step           Time
436
          20000       40.00000
437

    
438
   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
440
    3.86442e+03   -2.24993e+04   -1.86348e+04    2.95429e+03   -1.56806e+04
441
  Conserved En.    Temperature Pressure (bar)
442
   -1.55407e+04    2.96470e+02    5.49457e+02
443

    
444

    
445
DD  step 24999  vol min/aver 0.670  load imb.: force  9.0%
446
           Step           Time
447
          25000       50.00000
448

    
449
   Energies (kJ/mol)
450
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
451
    3.62556e+03   -2.22172e+04   -1.85917e+04    2.88841e+03   -1.57033e+04
452
  Conserved En.    Temperature Pressure (bar)
453
   -1.55192e+04    2.89859e+02   -7.52595e+02
454

    
455

    
456
DD  step 29999  vol min/aver 0.640  load imb.: force 11.2%
457
           Step           Time
458
          30000       60.00000
459

    
460
   Energies (kJ/mol)
461
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
462
    3.90394e+03   -2.26668e+04   -1.87629e+04    2.95992e+03   -1.58030e+04
463
  Conserved En.    Temperature Pressure (bar)
464
   -1.54977e+04    2.97035e+02    9.94135e+02
465

    
466

    
467
DD  step 34999  vol min/aver 0.661  load imb.: force 13.3%
468
           Step           Time
469
          35000       70.00000
470

    
471
   Energies (kJ/mol)
472
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
473
    3.90893e+03   -2.25727e+04   -1.86637e+04    3.09568e+03   -1.55681e+04
474
  Conserved En.    Temperature Pressure (bar)
475
   -1.54782e+04    3.10659e+02    7.00050e+02
476

    
477

    
478
DD  step 39999  vol min/aver 0.737  load imb.: force  9.1%
479
           Step           Time
480
          40000       80.00000
481

    
482
   Energies (kJ/mol)
483
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
484
    3.96747e+03   -2.26006e+04   -1.86332e+04    2.94919e+03   -1.56840e+04
485
  Conserved En.    Temperature Pressure (bar)
486
   -1.54532e+04    2.95958e+02    7.14098e+02
487

    
488

    
489
DD  step 44999  vol min/aver 0.637  load imb.: force 10.6%
490
           Step           Time
491
          45000       90.00000
492

    
493
   Energies (kJ/mol)
494
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
495
    3.79550e+03   -2.24481e+04   -1.86526e+04    2.92462e+03   -1.57280e+04
496
  Conserved En.    Temperature Pressure (bar)
497
   -1.54320e+04    2.93493e+02    2.25627e+01
498

    
499

    
500
DD  step 49999  vol min/aver 0.633  load imb.: force  7.2%
501
           Step           Time
502
          50000      100.00000
503

    
504
Writing checkpoint, step 50000 at Wed May 15 00:58:08 2019
505

    
506

    
507
   Energies (kJ/mol)
508
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
509
    3.84442e+03   -2.24616e+04   -1.86171e+04    2.90544e+03   -1.57117e+04
510
  Conserved En.    Temperature Pressure (bar)
511
   -1.54070e+04    2.91568e+02    3.00965e+02
512

    
513
	<======  ###############  ==>
514
	<====  A V E R A G E S  ====>
515
	<==  ###############  ======>
516

    
517
	Statistics over 50001 steps using 501 frames
518

    
519
   Energies (kJ/mol)
520
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
521
    3.81062e+03   -2.24902e+04   -1.86796e+04    2.98005e+03   -1.56996e+04
522
  Conserved En.    Temperature Pressure (bar)
523
   -1.55206e+04    2.99055e+02    1.25033e+02
524

    
525
   Total Virial (kJ/mol)
526
    9.47375e+02   -8.44842e+00    9.30347e+00
527
   -8.44603e+00    9.52364e+02    8.36890e+00
528
    9.27926e+00    8.33401e+00    9.44077e+02
529

    
530
   Pressure (bar)
531
    1.26952e+02    2.08812e+01   -2.56577e+01
532
    2.08746e+01    1.15589e+02   -1.70975e+01
533
   -2.55910e+01   -1.70014e+01    1.32559e+02
534

    
535

    
536
	M E G A - F L O P S   A C C O U N T I N G
537

    
538
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
539
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
540
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
541
 V&F=Potential and force  V=Potential only  F=Force only
542

    
543
 Computing:                               M-Number         M-Flops  % Flops
544
-----------------------------------------------------------------------------
545
 Pair Search distance check            1212.984108       10916.857     0.9
546
 NxN RF Elec. + LJ [F]                18319.545296      696142.721    55.1
547
 NxN RF Elec. + LJ [V&F]                185.328688       10007.749     0.8
548
 NxN RF Electrostatics [F]            17161.433904      532004.451    42.1
549
 NxN RF Electrostatics [V&F]            173.732176        6254.358     0.5
550
 Reset In Box                             3.001200           9.004     0.0
551
 CG-CoM                                   3.002400           9.007     0.0
552
 Virial                                   0.871740          15.691     0.0
553
 Stop-CM                                  0.602400           6.024     0.0
554
 Calc-Ekin                               12.002400         324.065     0.0
555
 Constraint-V                            76.288347         610.307     0.0
556
 Constraint-Vir                           0.765012          18.360     0.0
557
 Settle                                  25.429961        8213.877     0.6
558
-----------------------------------------------------------------------------
559
 Total                                                 1264532.472   100.0
560
-----------------------------------------------------------------------------
561

    
562

    
563
    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
564

    
565
 av. #atoms communicated per step for force:  2 x 6496.7
566
 av. #atoms communicated per step for LINCS:  2 x 350.7
567

    
568

    
569
 Dynamic load balancing report:
570
 DLB was turned on during the run due to measured imbalance.
571
 Average load imbalance: 10.0%.
572
 The balanceable part of the MD step is 54%, load imbalance is computed from this.
573
 Part of the total run time spent waiting due to load imbalance: 5.4%.
574
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 %
575

    
576
NOTE: 5.4 % of the available CPU time was lost due to load imbalance
577
      in the domain decomposition.
578

    
579

    
580
     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
581

    
582
On 12 MPI ranks, each using 2 OpenMP threads
583

    
584
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
585
                     Ranks Threads  Count      (s)         total sum    %
586
-----------------------------------------------------------------------------
587
 Domain decomp.        12    2       2501       0.558         34.761   8.3
588
 DD comm. load         12    2       2500       0.008          0.492   0.1
589
 DD comm. bounds       12    2       2499       0.023          1.417   0.3
590
 Neighbor search       12    2       2501       0.432         26.906   6.4
591
 Comm. coord.          12    2      47500       0.723         45.049  10.8
592
 Force                 12    2      50001       2.283        142.306  34.0
593
 Wait + Comm. F        12    2      50001       1.255         78.210  18.7
594
 NB X/F buffer ops.    12    2     145001       0.440         27.442   6.5
595
 Write traj.           12    2        101       0.003          0.207   0.0
596
 Update                12    2      50001       0.160          9.970   2.4
597
 Constraints           12    2      50003       0.637         39.719   9.5
598
 Comm. energies        12    2       5001       0.059          3.667   0.9
599
 Rest                                           0.142          8.858   2.1
600
-----------------------------------------------------------------------------
601
 Total                                          6.723        419.004 100.0
602
-----------------------------------------------------------------------------
603

    
604
               Core t (s)   Wall t (s)        (%)
605
       Time:      161.340        6.723     2399.9
606
                 (ns/day)    (hour/ns)
607
Performance:     1285.234        0.019
608
Finished mdrun on rank 0 Wed May 15 00:58:08 2019
609