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test_buffered.log

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

 
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Log file opened on Mon May 28 21:55:05 2018
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Host: c01n03  pid: 21094  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                        = -84930017
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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                          = 1.2
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   coulombtype                    = User
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   coulomb-modifier               = Potential-shift
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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                   = Potential-shift
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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           1.200 nm
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            two-body bonded interactions  (-rdd)   1.200 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           1.200 nm
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            two-body bonded interactions  (-rdd)   1.200 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: 1.2   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 1102 data points.
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Tabscale = 500 points/nm
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Read user tables from test_Protein_LIG.xvg with 1102 data points.
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Tabscale = 500 points/nm
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Read user tables from test.xvg with 1102 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: -3.186e-01 r^-6: -5.645e-01
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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: 10 x 11 x 8 cells
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Started mdrun on rank 0 Mon May 28 21:55:06 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    5.47770e+04   -4.86138e+05   -4.00277e+05    7.51228e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -3.25155e+05   -3.25155e+05    2.98516e+02    3.39691e+02    0.00000e+00
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DD  step 4 load imb.: force 92.5%
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step 15 Turning on dynamic load balancing, because the performance loss due to load imbalance is 12.6 %.
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DD  step 499  vol min/aver 0.395  load imb.: force  1.6%
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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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    1.38045e+03    3.46442e+03    4.50486e+03    2.24828e+02    1.58687e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
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    1.96323e+04    5.19247e+04   -4.83953e+05   -4.01234e+05    7.84452e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -3.22789e+05   -3.12134e+05    3.11719e+02    3.70211e+01    0.00000e+00
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DD  step 999  vol min/aver 0.406  load imb.: force  2.0%
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           Step           Time
417
           1000     2002.00000
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   Energies (kJ/mol)
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           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
421
    1.38874e+03    3.46900e+03    4.49823e+03    2.52070e+02    1.56253e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
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    1.97377e+04    5.13113e+04   -4.83047e+05   -4.00828e+05    7.79152e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -3.22912e+05   -2.98919e+05    3.09613e+02   -1.58249e+02    0.00000e+00
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DD  step 1499  vol min/aver 0.413  load imb.: force  1.7%
428

    
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           Step           Time
430
           1500     2003.00000
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   Energies (kJ/mol)
433
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
434
    1.41145e+03    3.47422e+03    4.60731e+03    2.28526e+02    1.54177e+03
435
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
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    1.97383e+04    5.10032e+04   -4.86350e+05   -4.04345e+05    7.95057e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -3.24840e+05   -2.87318e+05    3.15933e+02   -2.74065e+02    0.00000e+00
439

    
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DD  load balancing is limited by minimum cell size in dimension Y
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DD  step 1999  vol min/aver 0.431! load imb.: force  1.5%
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           Step           Time
444
           2000     2004.00000
445

    
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   Energies (kJ/mol)
447
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
448
    1.42671e+03    3.42959e+03    4.67012e+03    2.40779e+02    1.59861e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
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    1.97706e+04    5.25667e+04   -4.87515e+05   -4.03812e+05    7.85915e+04
451
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
452
   -3.25220e+05   -2.73868e+05    3.12300e+02   -6.21990e+00    0.00000e+00
453

    
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DD  step 2499  vol min/aver 0.417  load imb.: force  1.0%
455

    
456
           Step           Time
457
           2500     2005.00000
458

    
459
   Energies (kJ/mol)
460
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
461
    1.36217e+03    3.64890e+03    4.52527e+03    2.63455e+02    1.58638e+03
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     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
463
    1.96569e+04    5.23163e+04   -4.88135e+05   -4.04775e+05    7.83633e+04
464
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
465
   -3.26412e+05   -2.61686e+05    3.11393e+02   -1.92909e+01    0.00000e+00
466

    
467
DD  load balancing is limited by minimum cell size in dimension Y
468
DD  step 2999  vol min/aver 0.436! load imb.: force  1.0%
469

    
470
           Step           Time
471
           3000     2006.00000
472

    
473
   Energies (kJ/mol)
474
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
475
    1.35725e+03    3.56236e+03    4.57707e+03    2.54700e+02    1.58178e+03
476
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
477
    1.98216e+04    5.22178e+04   -4.87597e+05   -4.04224e+05    7.81229e+04
478
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
479
   -3.26101e+05   -2.47918e+05    3.10438e+02   -1.00299e+02    0.00000e+00
480

    
481
DD  load balancing is limited by minimum cell size in dimension Y
482
DD  step 3499  vol min/aver 0.407! load imb.: force  1.3%
483

    
484
           Step           Time
485
           3500     2007.00000
486

    
487
   Energies (kJ/mol)
488
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
489
    1.45649e+03    3.35209e+03    4.56334e+03    2.50289e+02    1.58108e+03
490
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
491
    1.95938e+04    5.41878e+04   -4.88500e+05   -4.03515e+05    7.78656e+04
492
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
493
   -3.25650e+05   -2.34179e+05    3.09415e+02    2.04071e+02    0.00000e+00
494

    
495
DD  load balancing is limited by minimum cell size in dimension Y
496
DD  step 3999  vol min/aver 0.432! load imb.: force  1.6%
497

    
498
           Step           Time
499
           4000     2008.00000
500

    
501
   Energies (kJ/mol)
502
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
503
    1.36458e+03    3.57050e+03    4.58480e+03    2.74835e+02    1.54655e+03
504
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
505
    1.93911e+04    5.31633e+04   -4.88983e+05   -4.05088e+05    7.82111e+04
506
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
507
   -3.26876e+05   -2.22409e+05    3.10789e+02   -4.82544e-01    0.00000e+00
508

    
509
DD  step 4499  vol min/aver 0.429  load imb.: force  1.2%
510

    
511
           Step           Time
512
           4500     2009.00000
513

    
514
   Energies (kJ/mol)
515
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
516
    1.33959e+03    3.63960e+03    4.63251e+03    2.59735e+02    1.56186e+03
517
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
518
    1.95253e+04    5.20460e+04   -4.87355e+05   -4.04350e+05    7.84044e+04
519
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
520
   -3.25946e+05   -2.08163e+05    3.11557e+02   -1.99222e+02    0.00000e+00
521

    
522
DD  step 4999  vol min/aver 0.429  load imb.: force  1.1%
523

    
524
           Step           Time
525
           5000     2010.00000
526

    
527
Writing checkpoint, step 5000 at Mon May 28 21:55:25 2018
528

    
529

    
530
   Energies (kJ/mol)
531
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
532
    1.27928e+03    3.45736e+03    4.67209e+03    2.42663e+02    1.61569e+03
533
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
534
    1.96952e+04    5.21218e+04   -4.90328e+05   -4.07244e+05    7.79434e+04
535
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
536
   -3.29301e+05   -1.98748e+05    3.09725e+02   -1.13087e+02    0.00000e+00
537

    
538
	<======  ###############  ==>
539
	<====  A V E R A G E S  ====>
540
	<==  ###############  ======>
541

    
542
	Statistics over 5001 steps using 51 frames
543

    
544
   Energies (kJ/mol)
545
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
546
    1.38184e+03    3.53703e+03    4.55987e+03    2.41192e+02    1.56995e+03
547
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
548
    1.96845e+04    5.23175e+04   -4.86626e+05   -4.03334e+05    7.80908e+04
549
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
550
   -3.25244e+05   -2.63186e+05    3.10310e+02   -6.25497e+01    0.00000e+00
551

    
552
   Total Virial (kJ/mol)
553
    2.64230e+04   -3.22407e+02    4.51986e+01
554
   -3.24789e+02    2.63799e+04    9.13017e+01
555
    4.94322e+01    9.64367e+01    2.69925e+04
556

    
557
   Pressure (bar)
558
   -4.71562e+01    4.09140e+01   -7.70031e+00
559
    4.11762e+01   -3.71684e+01   -1.39540e+01
560
   -8.16636e+00   -1.45193e+01   -1.03324e+02
561

    
562
  Epot (kJ/mol)        Coul-SR          LJ-SR        Coul-14          LJ-14   
563
Protein-Protein   -3.09145e+04   -3.06537e+03    2.00717e+04    1.55892e+03
564
    Protein-LIG    0.00000e+00    2.92809e+00    0.00000e+00    0.00000e+00
565
   Protein-rest   -1.24361e+04   -1.15340e+03    0.00000e+00    0.00000e+00
566
        LIG-LIG    5.18892e+01   -6.69474e+00   -3.87194e+02    1.10342e+01
567
       LIG-rest   -9.98480e+02   -3.66237e+01    0.00000e+00    0.00000e+00
568
      rest-rest   -4.42329e+05    5.65767e+04    0.00000e+00    0.00000e+00
569

    
570
  T-Protein_LIGT-Water_and_ions
571
    3.03341e+02    3.10851e+02
572

    
573

    
574
	M E G A - F L O P S   A C C O U N T I N G
575

    
576
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
577
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
578
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
579
 V&F=Potential and force  V=Potential only  F=Force only
580

    
581
 Computing:                               M-Number         M-Flops  % Flops
582
-----------------------------------------------------------------------------
583
 NB Elec. [V&F]                         698.810040         698.810     0.0
584
 NB Elec. [F]                         51419.466755       51419.467     2.0
585
 NB Elec. [W3,V&F]                       80.272395          80.272     0.0
586
 NB Elec. [W3,F]                       5904.905964        5904.906     0.2
587
 NB VdW & Elec. [V&F]                  1868.625107        1868.625     0.1
588
 NB VdW & Elec. [F]                  126760.556036      126760.556     4.9
589
 NB VdW & Elec. [W3,V&F]               1684.197060        1684.197     0.1
590
 NB VdW & Elec. [W3,F]               119824.796048      119824.796     4.6
591
 NB VdW & Elec. [W3-W3,V&F]           29376.902148       29376.902     1.1
592
 NB VdW & Elec. [W3-W3,F]           2133529.414658     2133529.415    82.1
593
 1,4 nonbonded interactions              22.429485        2018.654     0.1
594
 NS-Pairs                              3998.463693       83967.738     3.2
595
 Reset In Box                            11.124000          33.372     0.0
596
 CG-CoM                                  29.821792          89.465     0.0
597
 Bonds                                    4.590918         270.864     0.0
598
 Angles                                  15.633126        2626.365     0.1
599
 Propers                                 24.229845        5548.635     0.2
600
 Impropers                                1.910382         397.359     0.0
601
 Virial                                   1.883192          33.897     0.0
602
 Stop-CM                                  1.519392          15.194     0.0
603
 Calc-Ekin                               59.613792        1609.572     0.1
604
 Lincs                                    9.675824         580.549     0.0
605
 Lincs-Mat                               65.092384         260.370     0.0
606
 Constraint-V                           149.713826        1197.711     0.0
607
 Constraint-Vir                           1.826202          43.829     0.0
608
 Settle                                  93.358668       30154.850     1.2
609
-----------------------------------------------------------------------------
610
 Total                                                 2599996.370   100.0
611
-----------------------------------------------------------------------------
612

    
613

    
614
    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
615

    
616
 av. #atoms communicated per step for force:  2 x 86863.5
617
 av. #atoms communicated per step for LINCS:  3 x 224.0
618

    
619
 Average load imbalance: 4.2 %
620
 Part of the total run time spent waiting due to load imbalance: 1.3 %
621
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 5 %
622

    
623

    
624
     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
625

    
626
On 24 MPI ranks
627

    
628
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
629
                     Ranks Threads  Count      (s)         total sum    %
630
-----------------------------------------------------------------------------
631
 Domain decomp.        24    1       1000       1.090         65.382   5.5
632
 DD comm. load         24    1        999       0.104          6.234   0.5
633
 DD comm. bounds       24    1        998       0.072          4.303   0.4
634
 Neighbor search       24    1       1001       2.975        178.524  14.9
635
 Comm. coord.          24    1       5001       0.468         28.063   2.3
636
 Force                 24    1       5001       7.938        476.290  39.9
637
 Wait + Comm. F        24    1       5001       4.524        271.408  22.7
638
 Write traj.           24    1         11       0.020          1.179   0.1
639
 Update                24    1      17004       0.255         15.276   1.3
640
 Constraints           24    1      10002       1.152         69.148   5.8
641
 Comm. energies        24    1       4002       1.275         76.506   6.4
642
 Rest                                           0.043          2.606   0.2
643
-----------------------------------------------------------------------------
644
 Total                                         19.916       1194.921 100.0
645
-----------------------------------------------------------------------------
646

    
647
NOTE: 6 % of the run time was spent communicating energies,
648
      you might want to use the -gcom option of mdrun
649

    
650

    
651
               Core t (s)   Wall t (s)        (%)
652
       Time:      477.974       19.916     2400.0
653
                 (ns/day)    (hour/ns)
654
Performance:       43.392        0.553
655
Finished mdrun on rank 0 Mon May 28 21:55:26 2018