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run.log

Erik Lindahl, 12/04/2017 01:35 AM

 
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Log file opened on Mon Dec  4 01:32:30 2017
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Host: login1  pid: 2109  rank ID: 0  number of ranks:  1
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          :-) GROMACS - gmx mdrun, 2018-beta1-dev-20171129-2154a4f (-:
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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 2018-beta1-dev-20171129-2154a4f
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Executable:   /nethome/lindahl/Code/gmx/git/development/build/master/bin/gmx
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Data prefix:  /nethome/lindahl/Code/gmx/git/development/gromacs (source tree)
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Working dir:  /nethome/lindahl
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Command line:
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  gmx mdrun -nt 1 -v -deffnm run
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GROMACS version:    2018-beta1-dev-20171129-2154a4f
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GIT SHA1 hash:      2154a4f95ffccaf1c75315c0e69d056b394fa4ec
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Precision:          single
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Memory model:       64 bit
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MPI library:        thread_mpi
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support:        disabled
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SIMD instructions:  AVX2_256
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FFT library:        fftw-3.3.4-sse2-avx
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      hwloc-1.11.0
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Tracing support:    disabled
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Built on:           2017-12-04 00:30:09
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Built by:           lindahl@login1 [CMAKE]
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Build OS/arch:      Linux 4.4.0-98-generic x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz
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Build CPU family:   6   Model: 79   Stepping: 1
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Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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C compiler:         /usr/bin/cc GNU 5.4.0
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C compiler flags:    -march=core-avx2    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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C++ compiler:       /usr/bin/c++ GNU 5.4.0
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C++ compiler flags:  -march=core-avx2    -std=c++11  -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations -Wall  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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Running on 1 node with total 16 cores, 32 logical cores
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Hardware detected:
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  CPU info:
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    Vendor: Intel
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    Brand:  Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz
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    Family: 6   Model: 79   Stepping: 1
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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  Hardware topology: Full, with devices
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    Sockets, cores, and logical processors:
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      Socket  0: [   0  16] [   1  17] [   2  18] [   3  19] [   4  20] [   5  21] [   6  22] [   7  23]
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      Socket  1: [   8  24] [   9  25] [  10  26] [  11  27] [  12  28] [  13  29] [  14  30] [  15  31]
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    Numa nodes:
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      Node  0 (33618747392 bytes mem):   0  16   1  17   2  18   3  19   4  20   5  21   6  22   7  23
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      Node  1 (33820061696 bytes mem):   8  24   9  25  10  26  11  27  12  28  13  29  14  30  15  31
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      Latency:
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               0     1
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         0  1.00  2.10
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         1  2.10  1.00
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    Caches:
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      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
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      L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
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      L3: 20971520 bytes, linesize 64 bytes, assoc. 20, shared 16 ways
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    PCI devices:
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      0000:03:00.0  Id: 8086:1528  Class: 0x0200  Numa: 0
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      0000:03:00.1  Id: 8086:1528  Class: 0x0200  Numa: 0
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      0000:00:11.4  Id: 8086:8d62  Class: 0x0106  Numa: 0
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      0000:07:00.0  Id: 1a03:2000  Class: 0x0300  Numa: 0
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      0000:00:1f.2  Id: 8086:8d02  Class: 0x0106  Numa: 0
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
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Lindahl
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GROMACS: High performance molecular simulations through multi-level
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parallelism from laptops to supercomputers
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SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
104
GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
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GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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Input Parameters:
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   integrator                     = md
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   tinit                          = 0
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   dt                             = 0.005
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   nsteps                         = 2000
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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                        = -1492730490
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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                        = 100
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   nstvout                        = 100
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   nstfout                        = 100
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   nstlog                         = 100
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   nstcalcenergy                  = 50
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   nstenergy                      = 100
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   nstxout-compressed             = 200000
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
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   nstlist                        = 10
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   ns-type                        = Grid
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   pbc                            = xyz
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   periodic-molecules             = false
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   verlet-buffer-tolerance        = 0.005
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   rlist                          = 1.035
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   coulombtype                    = PME
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   coulomb-modifier               = Potential-shift
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   rcoulomb-switch                = 0
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   rcoulomb                       = 1
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   epsilon-r                      = 1
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   epsilon-rf                     = inf
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   vdw-type                       = Cut-off
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   vdw-modifier                   = Potential-shift
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   rvdw-switch                    = 0
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   rvdw                           = 1
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   DispCorr                       = AllEnerPres
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   table-extension                = 1
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   fourierspacing                 = 0.125
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   fourier-nx                     = 40
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   fourier-ny                     = 40
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   fourier-nz                     = 40
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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                         = V-rescale
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   nsttcouple                     = 10
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = Berendsen
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   pcoupltype                     = Semiisotropic
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   nstpcouple                     = 10
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   tau-p                          = 5
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   compressibility (3x3):
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      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
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   ref-p (3x3):
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      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
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   refcoord-scaling               = COM
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   posres-com (3):
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      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = false
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = true
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 4
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   lincs-iter                     = 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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   awh                            = false
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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = No
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   disre-weighting                = Conservative
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   disre-mixed                    = false
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   dr-fc                          = 1000
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   dr-tau                         = 0
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   nstdisreout                    = 100
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   orire-fc                       = 0
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   orire-tau                      = 0
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   nstorireout                    = 100
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   free-energy                    = no
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   cos-acceleration               = 0
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   deform (3x3):
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      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   simulated-tempering            = false
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   swapcoords                     = no
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   userint1                       = 0
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   userint2                       = 0
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   userint3                       = 0
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   userint4                       = 0
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   userreal1                      = 0
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   userreal2                      = 0
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   userreal3                      = 0
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   userreal4                      = 0
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   applied-forces:
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     electric-field:
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grpopts:
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   nrdf:     592.872     13341.1
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   ref-t:         300         300
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   tau-t:         0.5         0.5
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annealing:          No          No
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annealing-npoints:           0           0
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   acc:	           0           0           0
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   nfreeze:           N           N           N
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   energygrp-flags[  0]: 0
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Changing nstlist from 10 to 50, rlist from 1.035 to 1.19
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Using 1 MPI thread
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Using 1 OpenMP thread 
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System total charge: 0.000
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Will do PME sum in reciprocal space for electrostatic interactions.
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
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A smooth particle mesh Ewald method
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J. Chem. Phys. 103 (1995) pp. 8577-8592
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-------- -------- --- Thank You --- -------- --------
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Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
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Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
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Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
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Long Range LJ corr.: <C6> 3.0799e-04, <C12> 3.0817e-07
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Generated table with 1095 data points for Ewald.
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Tabscale = 500 points/nm
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Generated table with 1095 data points for LJ6.
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Tabscale = 500 points/nm
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Generated table with 1095 data points for LJ12.
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Tabscale = 500 points/nm
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Generated table with 1095 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1095 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1095 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Using SIMD 4x8 nonbonded short-range kernels
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Using a dual 4x8 pair-list setup updated with dynamic pruning:
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  outer list: updated every 50 steps, buffer 0.190 nm, rlist 1.190 nm
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  inner list: updated every  6 steps, buffer 0.002 nm, rlist 1.002 nm
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At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
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  outer list: updated every 50 steps, buffer 0.354 nm, rlist 1.354 nm
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  inner list: updated every  6 steps, buffer 0.053 nm, rlist 1.053 nm
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Using Lorentz-Berthelot Lennard-Jones combination rule
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NOTE: Thread affinity setting failed. This can cause performance degradation.
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      If you think your settings are correct, ask on the gmx-users list.
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Initializing 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 346
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78 constraints are involved in constraint triangles,
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will apply an additional matrix expansion of order 4 for couplings
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between constraints inside triangles
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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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Intra-simulation communication will occur every 10 steps.
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Center of mass motion removal mode is Linear
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We have the following groups for center of mass motion removal:
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  0:  System
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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G. Bussi, D. Donadio and M. Parrinello
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Canonical sampling through velocity rescaling
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J. Chem. Phys. 126 (2007) pp. 014101
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-------- -------- --- Thank You --- -------- --------
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There are: 6985 Atoms
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There are: 309 VSites
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Started mdrun on rank 0 Mon Dec  4 01:32:33 2017
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           Step           Time
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              0        0.00000
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    6.56428e+02    1.30254e+03    3.41272e+01    6.60833e+02    7.76186e+03
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        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
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    1.09802e+04   -9.34229e+02   -1.06678e+05    9.35155e+02   -8.52814e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
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    2.25297e+04   -6.27516e+04   -6.27565e+04    3.88934e+02   -2.11806e+02
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 Pressure (bar)   Constr. rmsd
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    1.38499e+03    3.15779e-05
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           Step           Time
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            100        0.50000
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    6.48282e+02    1.27624e+03    5.39398e+01    6.59025e+02    7.67741e+03
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        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
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    1.07536e+04   -9.30876e+02   -1.08097e+05    8.82338e+02   -8.70769e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
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    2.07187e+04   -6.63582e+04   -6.27749e+04    3.57670e+02   -2.10290e+02
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 Pressure (bar)   Constr. rmsd
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    3.69412e+02    2.64492e-05
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Received the INT signal, stopping within 50 steps
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           Step           Time
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            200        1.00000
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Writing checkpoint, step 200 at Mon Dec  4 01:32:34 2017
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    5.81807e+02    1.27331e+03    4.19219e+01    6.28922e+02    7.71442e+03
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        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
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    1.16428e+04   -9.29672e+02   -1.11543e+05    7.74185e+02   -8.98152e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
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    1.98363e+04   -6.99790e+04   -6.27422e+04    3.42437e+02   -2.09747e+02
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 Pressure (bar)   Constr. rmsd
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    1.35692e+02    2.85490e-05
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	<======  ###############  ==>
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	<====  A V E R A G E S  ====>
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	<==  ###############  ======>
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	Statistics over 201 steps using 5 frames
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
438
    6.12248e+02    1.29028e+03    4.59742e+01    6.40371e+02    7.71967e+03
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        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
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    1.11243e+04   -9.31383e+02   -1.08727e+05    8.53733e+02   -8.73719e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
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    2.09791e+04   -6.63928e+04   -6.27685e+04    3.62165e+02   -2.10519e+02
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 Pressure (bar)   Constr. rmsd
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    6.04855e+02    0.00000e+00
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          Box-X          Box-Y          Box-Z
447
    4.70318e+00    4.70318e+00    3.32528e+00
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   Total Virial (kJ/mol)
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    6.01211e+03    6.94740e+01   -2.03662e+02
451
    6.96329e+01    5.70911e+03    2.05099e+01
452
   -2.03808e+02    2.03702e+01    5.24376e+03
453

    
454
   Pressure (bar)
455
    4.36212e+02   -2.25911e+01    8.86319e+01
456
   -2.26631e+01    5.83398e+02    6.26859e+00
457
    8.86978e+01    6.33153e+00    7.94956e+02
458

    
459
       T-villin          T-SOL
460
    3.42452e+02    3.63042e+02
461

    
462

    
463
	M E G A - F L O P S   A C C O U N T I N G
464

    
465
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
466
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
467
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
468
 V&F=Potential and force  V=Potential only  F=Force only
469

    
470
 Computing:                               M-Number         M-Flops  % Flops
471
-----------------------------------------------------------------------------
472
 Pair Search distance check              17.304964         155.745     0.2
473
 NxN Ewald Elec. + LJ [F]               547.939952       36164.037    50.6
474
 NxN Ewald Elec. + LJ [V&F]              13.961616        1493.893     2.1
475
 NxN Ewald Elec. [F]                    462.096656       28187.896    39.4
476
 NxN Ewald Elec. [V&F]                   11.793072         990.618     1.4
477
 1,4 nonbonded interactions               0.303912          27.352     0.0
478
 Calc Weights                             4.398282         158.338     0.2
479
 Spread Q Bspline                        93.830016         187.660     0.3
480
 Gather F Bspline                        93.830016         562.980     0.8
481
 3D-FFT                                 410.767620        3286.141     4.6
482
 Solve PME                                0.321600          20.582     0.0
483
 Shift-X                                  0.036470           0.219     0.0
484
 Angles                                   0.181302          30.459     0.0
485
 Propers                                  0.299490          68.583     0.1
486
 Impropers                                0.023718           4.933     0.0
487
 Virial                                   0.154119           2.774     0.0
488
 Stop-CM                                  0.021882           0.219     0.0
489
 P-Coupling                               0.153174           0.919     0.0
490
 Calc-Ekin                                0.306348           8.271     0.0
491
 Lincs                                    0.069546           4.173     0.0
492
 Lincs-Mat                                1.384488           5.538     0.0
493
 Constraint-V                             1.480164          11.841     0.0
494
 Constraint-Vir                           0.147378           3.537     0.0
495
 Settle                                   0.447024         144.389     0.2
496
 Virtual Site 3                           0.010212           0.378     0.0
497
 Virtual Site 3fd                         0.013986           1.329     0.0
498
 Virtual Site 3fad                        0.002220           0.391     0.0
499
 Virtual Site 3out                        0.033300           2.897     0.0
500
 Virtual Site 4fdn                        0.008880           2.256     0.0
501
-----------------------------------------------------------------------------
502
 Total                                                   71528.347   100.0
503
-----------------------------------------------------------------------------
504

    
505

    
506
     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
507

    
508
On 1 MPI rank
509

    
510
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
511
                     Ranks Threads  Count      (s)         total sum    %
512
-----------------------------------------------------------------------------
513
 Vsite constr.          1    1        201       0.003          0.006   0.2
514
 Neighbor search        1    1          5       0.074          0.157   4.4
515
 Force                  1    1        201       1.196          2.514  70.3
516
 PME mesh               1    1        201       0.319          0.671  18.8
517
 NB X/F buffer ops.     1    1        397       0.007          0.015   0.4
518
 Vsite spread           1    1        222       0.004          0.009   0.2
519
 Write traj.            1    1          3       0.067          0.141   3.9
520
 Update                 1    1        201       0.004          0.009   0.3
521
 Constraints            1    1        201       0.019          0.040   1.1
522
 Rest                                           0.006          0.012   0.3
523
-----------------------------------------------------------------------------
524
 Total                                          1.701          3.575 100.0
525
-----------------------------------------------------------------------------
526
 Breakdown of PME mesh computation
527
-----------------------------------------------------------------------------
528
 PME spread             1    1        201       0.091          0.191   5.3
529
 PME gather             1    1        201       0.079          0.166   4.7
530
 PME 3D-FFT             1    1        402       0.122          0.255   7.1
531
 PME solve Elec         1    1        201       0.028          0.058   1.6
532
-----------------------------------------------------------------------------
533

    
534
               Core t (s)   Wall t (s)        (%)
535
       Time:        1.701        1.701      100.0
536
                 (ns/day)    (hour/ns)
537
Performance:       51.052        0.470
538
Finished mdrun on rank 0 Mon Dec  4 01:32:35 2017