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test_unbuffered.log

unix2doced - Yu Du, 05/28/2018 04:21 PM

 
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Log file opened on Mon May 28 22:00:05 2018
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Host: c01n03  pid: 20455  rank ID: 0  number of ranks:  1
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                      :-) GROMACS - gmx mdrun, 2016.4 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
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 Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  
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 Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
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    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
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  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff    Erik Marklund   
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   Teemu Murtola       Szilard Pall       Sander Pronk      Roland Schulz   
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  Alexey Shvetsov     Michael Shirts     Alfons Sijbers     Peter Tieleman  
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  Teemu Virolainen  Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2017, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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GROMACS:      gmx mdrun, version 2016.4
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Executable:   /share/home/para008/software/gromacs-2016.4/bin/gmx
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Data prefix:  /share/home/para008/software/gromacs-2016.4
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Working dir:  /share/home/para008/dir-test/md_dir
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Command line:
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  gmx mdrun -quiet -notunepme -pin on -pinoffset 0 -ntomp 1 -ntmpi 24 -deffnm test
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GROMACS version:    2016.4
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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 = 32)
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GPU support:        disabled
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SIMD instructions:  AVX2_256
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FFT library:        fftw-3.3.6-pl2-sse2-avx
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      disabled
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Tracing support:    disabled
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Built on:           Fri Dec 29 10:51:30 CST 2017
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Built by:           para008@c01n03 [CMAKE]
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Build OS/arch:      Linux 2.6.32-696.el6.x86_64 x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
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Build CPU family:   6   Model: 63   Stepping: 2
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Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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C compiler:         /share/home/para008/software/gcc-6.3.0/bin/gcc-6.3 GNU 6.3.0
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C compiler flags:    -march=core-avx2   -Wl,-rpath -Wl,/share/home/para008/software/gcc-6.3.0/lib64  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /share/home/para008/software/gcc-6.3.0/bin/g++-6.3 GNU 6.3.0
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C++ compiler flags:  -march=core-avx2    -std=c++0x   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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Running on 1 node with total 24 cores, 24 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 E5-2680 v3 @ 2.50GHz
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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 htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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    SIMD instructions most likely to fit this hardware: AVX2_256
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    SIMD instructions selected at GROMACS compile time: AVX2_256
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  Hardware topology: Basic
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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]
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      Socket  1: [  12] [  13] [  14] [  15] [  16] [  17] [  18] [  19] [  20] [  21] [  22] [  23]
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
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Lindahl
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GROMACS: High performance molecular simulations through multi-level
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parallelism from laptops to supercomputers
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SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
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GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
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GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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Input Parameters:
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   integrator                     = md-vv
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   tinit                          = 2000
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   dt                             = 0.002
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   nsteps                         = 5000
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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                        = -1326379975
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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                         = 500
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   nstcalcenergy                  = 100
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   nstenergy                      = 500
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   nstxout-compressed             = 500
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Group
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   nstlist                        = 5
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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                          = 1.1
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   coulombtype                    = User
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   coulomb-modifier               = None
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   rcoulomb-switch                = 0
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   rcoulomb                       = 1.1
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   epsilon-r                      = 1
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   epsilon-rf                     = inf
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   vdw-type                       = User
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   vdw-modifier                   = None
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   rvdw-switch                    = 0
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   rvdw                           = 1.1
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.12
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   fourier-nx                     = 0
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   fourier-ny                     = 0
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   fourier-nz                     = 0
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   pme-order                      = 4
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   ewald-rtol                     = 1e-05
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   ewald-rtol-lj                  = 0.001
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   lj-pme-comb-rule               = Geometric
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   ewald-geometry                 = 0
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   epsilon-surface                = 0
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   implicit-solvent               = No
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   gb-algorithm                   = Still
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   nstgbradii                     = 1
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   rgbradii                       = 1
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   gb-epsilon-solvent             = 80
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   gb-saltconc                    = 0
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   gb-obc-alpha                   = 1
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   gb-obc-beta                    = 0.8
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   gb-obc-gamma                   = 4.85
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   gb-dielectric-offset           = 0.009
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   sa-algorithm                   = Ace-approximation
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   sa-surface-tension             = 2.05016
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   tcoupl                         = Nose-Hoover
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   nsttcouple                     = 5
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   nh-chain-length                = 10
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = No
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   pcoupltype                     = Isotropic
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   nstpcouple                     = -1
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   tau-p                          = 1
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   compressibility (3x3):
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      compressibility[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   ref-p (3x3):
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      ref-p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   refcoord-scaling               = No
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   posres-com (3):
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      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = false
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = true
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 6
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   lincs-iter                     = 2
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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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   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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   E-x:
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      n = 0
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   E-xt:
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      n = 0
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   E-y:
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      n = 0
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   E-yt:
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      n = 0
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   E-z:
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      n = 0
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   E-zt:
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      n = 0
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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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grpopts:
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   nrdf:     4358.78     56175.2
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   ref-t:         300         300
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   tau-t:           1           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 2 0
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   energygrp-flags[  1]: 2 0 0
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   energygrp-flags[  2]: 0 0 0
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Initializing Domain Decomposition on 24 ranks
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Dynamic load balancing: auto
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Initial maximum inter charge-group distances:
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    two-body bonded interactions: 0.410 nm, LJ-14, atoms 7 10
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  multi-body bonded interactions: 0.410 nm, Proper Dih., atoms 7 10
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Minimum cell size due to bonded interactions: 0.451 nm
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Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 0.219 nm
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Estimated maximum distance required for P-LINCS: 0.219 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 24 cells with a minimum initial size of 0.564 nm
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The maximum allowed number of cells is: X 10 Y 10 Z 9
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Domain decomposition grid 6 x 4 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 1
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The initial domain decomposition cell size is: X 1.02 nm Y 1.54 nm
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.100 nm
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            two-body bonded interactions  (-rdd)   1.100 nm
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          multi-body bonded interactions  (-rdd)   1.024 nm
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  atoms separated by up to 7 constraints  (-rcon)  1.024 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 2 Y 2
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The minimum size for domain decomposition cells is 0.717 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 0.70 Y 0.47
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.100 nm
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            two-body bonded interactions  (-rdd)   1.100 nm
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          multi-body bonded interactions  (-rdd)   0.717 nm
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  atoms separated by up to 7 constraints  (-rcon)  0.717 nm
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Using 24 MPI threads
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NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
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removed in a future release when 'verlet' supports all interaction forms.
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Table routines are used for coulomb: true
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Table routines are used for vdw:     true
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Cut-off's:   NS: 1.1   Coulomb: 1.1   LJ: 1.1
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System total charge: -0.000
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Read user tables from test.xvg with 1051 data points.
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Tabscale = 500 points/nm
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Read user tables from test_Protein_LIG.xvg with 1051 data points.
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Tabscale = 500 points/nm
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Read user tables from test.xvg with 1051 data points.
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Tabscale = 500 points/nm
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Enabling SPC-like water optimization for 9334 molecules.
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Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00
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Pinning threads with an auto-selected logical core stride of 1
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Initializing Parallel LINear Constraint Solver
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess
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P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 116-122
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-------- -------- --- Thank You --- -------- --------
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The number of constraints is 837
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There are inter charge-group constraints,
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will communicate selected coordinates each lincs iteration
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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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
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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 5 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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There are: 29792 Atoms
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Atom distribution over 24 domains: av 1241 stddev 38 min 1216 max 1309
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Grid: 9 x 10 x 8 cells
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Started mdrun on rank 0 Mon May 28 22:00:06 2018
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           Step           Time
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              0     2000.00000
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   Energies (kJ/mol)
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           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
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    1.48161e+03    3.51806e+03    4.47456e+03    2.10320e+02    1.59438e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
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    1.98047e+04    5.51090e+04   -4.89485e+05   -4.03292e+05    7.51228e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -3.28170e+05   -3.28170e+05    2.98516e+02    3.57101e+02    0.00000e+00
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DD  step 4 load imb.: force 100.3%
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step 15 Turning on dynamic load balancing, because the performance loss due to load imbalance is 11.5 %.
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DD  load balancing is limited by minimum cell size in dimension Y
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DD  step 499  vol min/aver 0.403! load imb.: force  0.9%
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           Step           Time
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            500     2001.00000
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   Energies (kJ/mol)
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           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
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    1.43700e+03    3.58766e+03    4.59329e+03    2.45079e+02    1.57019e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
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    1.97253e+04    5.22962e+04   -4.86244e+05   -4.02789e+05    7.92513e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -3.23538e+05   -3.10247e+05    3.14922e+02    1.50525e+02    0.00000e+00
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DD  step 999  vol min/aver 0.403  load imb.: force  0.8%
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           Step           Time
418
           1000     2002.00000
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   Energies (kJ/mol)
421
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
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    1.39922e+03    3.59764e+03    4.54947e+03    2.25372e+02    1.55797e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
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    1.97612e+04    5.28473e+04   -4.89775e+05   -4.05837e+05    7.96809e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -3.26156e+05   -2.96695e+05    3.16629e+02    7.76059e+01    0.00000e+00
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DD  step 1499  vol min/aver 0.403  load imb.: force  0.9%
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           Step           Time
431
           1500     2003.00000
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   Energies (kJ/mol)
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           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
435
    1.45941e+03    3.64430e+03    4.67209e+03    2.77926e+02    1.60616e+03
436
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
437
    1.96713e+04    5.12399e+04   -4.86063e+05   -4.03492e+05    7.99682e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -3.23524e+05   -2.77840e+05    3.17770e+02   -6.23797e+01    0.00000e+00
440

    
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DD  step 1999  vol min/aver 0.403  load imb.: force  1.5%
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           Step           Time
444
           2000     2004.00000
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   Energies (kJ/mol)
447
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
448
    1.30539e+03    3.68729e+03    4.66266e+03    2.29773e+02    1.59784e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
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    1.97557e+04    5.12936e+04   -4.87395e+05   -4.04863e+05    8.01137e+04
451
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -3.24749e+05   -2.62117e+05    3.18349e+02   -1.91439e+02    0.00000e+00
453

    
454
DD  step 2499  vol min/aver 0.411  load imb.: force  1.4%
455

    
456
           Step           Time
457
           2500     2005.00000
458

    
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   Energies (kJ/mol)
460
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
461
    1.35117e+03    3.85091e+03    4.60427e+03    2.61884e+02    1.58015e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
463
    1.96594e+04    5.19426e+04   -4.89060e+05   -4.05810e+05    8.01164e+04
464
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
465
   -3.25694e+05   -2.46318e+05    3.18360e+02   -6.29796e+01    0.00000e+00
466

    
467
DD  step 2999  vol min/aver 0.396  load imb.: force  1.6%
468

    
469
           Step           Time
470
           3000     2006.00000
471

    
472
   Energies (kJ/mol)
473
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
474
    1.41893e+03    3.60254e+03    4.63085e+03    2.37935e+02    1.55343e+03
475
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
476
    1.94592e+04    5.25074e+04   -4.90564e+05   -4.07154e+05    8.02796e+04
477
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
478
   -3.26874e+05   -2.30878e+05    3.19008e+02   -3.56123e+01    0.00000e+00
479

    
480
DD  step 3499  vol min/aver 0.416  load imb.: force  1.3%
481

    
482
           Step           Time
483
           3500     2007.00000
484

    
485
   Energies (kJ/mol)
486
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
487
    1.39639e+03    3.57057e+03    4.61794e+03    2.65898e+02    1.54137e+03
488
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
489
    1.95134e+04    5.27258e+04   -4.88924e+05   -4.05292e+05    8.02418e+04
490
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
491
   -3.25051e+05   -2.12774e+05    3.18858e+02    7.57684e+01    0.00000e+00
492

    
493
DD  step 3999  vol min/aver 0.424  load imb.: force  1.6%
494

    
495
           Step           Time
496
           4000     2008.00000
497

    
498
   Energies (kJ/mol)
499
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
500
    1.35530e+03    3.43172e+03    4.63866e+03    2.86298e+02    1.59370e+03
501
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
502
    1.97075e+04    5.25204e+04   -4.88886e+05   -4.05352e+05    7.98671e+04
503
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
504
   -3.25485e+05   -1.96697e+05    3.17369e+02    5.05212e+01    0.00000e+00
505

    
506
DD  step 4499  vol min/aver 0.423  load imb.: force  2.0%
507

    
508
           Step           Time
509
           4500     2009.00000
510

    
511
   Energies (kJ/mol)
512
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
513
    1.27987e+03    3.55470e+03    4.55287e+03    2.32038e+02    1.58314e+03
514
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
515
    1.97327e+04    5.29338e+04   -4.90269e+05   -4.06400e+05    8.01401e+04
516
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
517
   -3.26260e+05   -1.81158e+05    3.18454e+02    1.54465e+02    0.00000e+00
518

    
519
DD  step 4999  vol min/aver 0.409  load imb.: force  1.8%
520

    
521
           Step           Time
522
           5000     2010.00000
523

    
524
Writing checkpoint, step 5000 at Mon May 28 22:00:20 2018
525

    
526

    
527
   Energies (kJ/mol)
528
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
529
    1.27814e+03    3.56242e+03    4.63287e+03    2.57570e+02    1.53697e+03
530
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
531
    1.95812e+04    5.27070e+04   -4.89086e+05   -4.05530e+05    7.93597e+04
532
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
533
   -3.26170e+05   -1.64599e+05    3.15353e+02    1.74367e+02    0.00000e+00
534

    
535
	<======  ###############  ==>
536
	<====  A V E R A G E S  ====>
537
	<==  ###############  ======>
538

    
539
	Statistics over 5001 steps using 51 frames
540

    
541
   Energies (kJ/mol)
542
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
543
    1.39299e+03    3.59139e+03    4.61856e+03    2.51254e+02    1.56620e+03
544
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
545
    1.97190e+04    5.23944e+04   -4.88823e+05   -4.05289e+05    7.94686e+04
546
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
547
   -3.25821e+05   -2.49528e+05    3.15785e+02    1.65515e+01    0.00000e+00
548

    
549
   Total Virial (kJ/mol)
550
    2.63054e+04   -1.11658e+02    1.80111e+02
551
   -1.20452e+02    2.65845e+04   -4.37282e+02
552
    1.74587e+02   -4.36210e+02    2.61277e+04
553

    
554
   Pressure (bar)
555
    1.58178e+01    1.98550e+01   -2.07894e+01
556
    2.08232e+01   -8.15119e+00    5.40439e+01
557
   -2.01813e+01    5.39259e+01    4.19878e+01
558

    
559
  Epot (kJ/mol)        Coul-SR          LJ-SR        Coul-14          LJ-14   
560
Protein-Protein   -3.57440e+04   -2.98691e+03    2.01013e+04    1.55602e+03
561
    Protein-LIG    0.00000e+00    2.48770e+00    0.00000e+00    0.00000e+00
562
   Protein-rest   -1.14148e+04   -1.12670e+03    0.00000e+00    0.00000e+00
563
        LIG-LIG    8.43552e+01   -7.09268e+00   -3.82322e+02    1.01840e+01
564
       LIG-rest   -1.00285e+03   -3.26795e+01    0.00000e+00    0.00000e+00
565
      rest-rest   -4.40746e+05    5.65453e+04    0.00000e+00    0.00000e+00
566

    
567
  T-Protein_LIGT-Water_and_ions
568
    3.10253e+02    3.16214e+02
569

    
570

    
571
	M E G A - F L O P S   A C C O U N T I N G
572

    
573
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
574
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
575
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
576
 V&F=Potential and force  V=Potential only  F=Force only
577

    
578
 Computing:                               M-Number         M-Flops  % Flops
579
-----------------------------------------------------------------------------
580
 NB Elec. [V&F]                         522.999640         523.000     0.0
581
 NB Elec. [F]                         38441.816912       38441.817     1.9
582
 NB Elec. [W3,V&F]                       63.592232          63.592     0.0
583
 NB Elec. [W3,F]                       4674.745326        4674.745     0.2
584
 NB VdW & Elec. [V&F]                  1499.882837        1499.883     0.1
585
 NB VdW & Elec. [F]                  101721.512806      101721.513     5.0
586
 NB VdW & Elec. [W3,V&F]               1267.884060        1267.884     0.1
587
 NB VdW & Elec. [W3,F]                90244.402814       90244.403     4.4
588
 NB VdW & Elec. [W3-W3,V&F]           22916.062528       22916.063     1.1
589
 NB VdW & Elec. [W3-W3,F]           1664171.964188     1664171.964    81.6
590
 1,4 nonbonded interactions              22.429485        2018.654     0.1
591
 NS-Pairs                              3299.424795       69287.921     3.4
592
 Reset In Box                            11.124000          33.372     0.0
593
 CG-CoM                                  29.821792          89.465     0.0
594
 Bonds                                    4.590918         270.864     0.0
595
 Angles                                  15.633126        2626.365     0.1
596
 Propers                                 24.229845        5548.635     0.3
597
 Impropers                                1.910382         397.359     0.0
598
 Virial                                   1.883192          33.897     0.0
599
 Stop-CM                                  1.519392          15.194     0.0
600
 Calc-Ekin                               59.613792        1609.572     0.1
601
 Lincs                                    9.766924         586.015     0.0
602
 Lincs-Mat                               66.644608         266.578     0.0
603
 Constraint-V                           149.804926        1198.439     0.1
604
 Constraint-Vir                           1.827260          43.854     0.0
605
 Settle                                  93.358668       30154.850     1.5
606
-----------------------------------------------------------------------------
607
 Total                                                 2039705.899   100.0
608
-----------------------------------------------------------------------------
609

    
610

    
611
    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
612

    
613
 av. #atoms communicated per step for force:  2 x 77560.1
614
 av. #atoms communicated per step for LINCS:  3 x 242.6
615

    
616
 Average load imbalance: 3.1 %
617
 Part of the total run time spent waiting due to load imbalance: 1.0 %
618
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 2 %
619

    
620

    
621
     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
622

    
623
On 24 MPI ranks
624

    
625
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
626
                     Ranks Threads  Count      (s)         total sum    %
627
-----------------------------------------------------------------------------
628
 Domain decomp.        24    1       1000       0.994         59.659   6.6
629
 DD comm. load         24    1        999       0.122          7.330   0.8
630
 DD comm. bounds       24    1        998       0.078          4.653   0.5
631
 Neighbor search       24    1       1001       2.509        150.543  16.7
632
 Comm. coord.          24    1       5001       0.474         28.464   3.2
633
 Force                 24    1       5001       6.189        371.346  41.3
634
 Wait + Comm. F        24    1       5001       1.868        112.097  12.5
635
 Write traj.           24    1         11       0.018          1.089   0.1
636
 Update                24    1      17004       0.255         15.316   1.7
637
 Constraints           24    1      10002       1.044         62.636   7.0
638
 Comm. energies        24    1       4002       1.404         84.256   9.4
639
 Rest                                           0.036          2.174   0.2
640
-----------------------------------------------------------------------------
641
 Total                                         14.993        899.563 100.0
642
-----------------------------------------------------------------------------
643

    
644
NOTE: 9 % of the run time was spent communicating energies,
645
      you might want to use the -gcom option of mdrun
646

    
647

    
648
               Core t (s)   Wall t (s)        (%)
649
       Time:      359.829       14.993     2400.0
650
                 (ns/day)    (hour/ns)
651
Performance:       57.639        0.416
652
Finished mdrun on rank 0 Mon May 28 22:00:21 2018