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Szilárd Páll, 06/11/2019 12:09 AM

 
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           :-) GROMACS - gmx mdrun, 2019.3-dev-20190610-7e3521c2d (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
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    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
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 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
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  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
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  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
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    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
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  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
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    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
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    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
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   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
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 Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2018, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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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 2019.3-dev-20190610-7e3521c2d
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Executable:   /home/pszilard/projects/gromacs/gromacs-19/build_clang7_ocl/bin/gmx
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Data prefix:  /home/pszilard/projects/gromacs/gromacs-19 (source tree)
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Working dir:  /home/pszilard/projects/gromacs/regressiontests-19/complex/position-restraints
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Process ID:   10249
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Command line:
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  gmx mdrun -ntmpi 1 -notunepme
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GROMACS version:    2019.3-dev-20190610-7e3521c2d
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GIT SHA1 hash:      7e3521c2dd4d57f1cd730f45afac12decb2abd8e
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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:        OpenCL
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SIMD instructions:  AVX2_256
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FFT library:        fftw-3.3.7-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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C compiler:         /home/pszilard/programs/clang/7.0.0/bin/clang Clang 7.0.0
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C compiler flags:    -mavx2 -mfma    -Wall -Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG  
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C++ compiler:       /home/pszilard/programs/clang/7.0.0/bin/clang++ Clang 7.0.0
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C++ compiler flags:  -mavx2 -mfma    -std=c++11  -Wdeprecated -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-prototypes -Wall  -O3 -DNDEBUG  
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OpenCL include dir: /usr/include
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OpenCL library:     /usr/lib/x86_64-linux-gnu/libOpenCL.so
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OpenCL version:     2.2
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Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
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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) Core(TM) i7-8550U CPU @ 1.80GHz
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    Family: 6   Model: 142   Stepping: 10
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel 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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  Hardware topology: Basic
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    Sockets, cores, and logical processors:
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      Socket  0: [   0   4] [   1   5] [   2   6] [   3   7]
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  GPU info:
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    Number of GPUs detected: 1
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    #0: name: Intel(R) Gen9 HD Graphics NEO, vendor: Intel(R) Corporation, device version: OpenCL 2.1 NEO , stat: compatible
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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
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   tinit                          = 0
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   dt                             = 0.002
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   nsteps                         = 10
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   init-step                      = 0
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   simulation-part                = 1
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   comm-mode                      = None
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   nstcomm                        = 0
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   bd-fric                        = 0
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   ld-seed                        = 1993
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   emtol                          = 20
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   emstep                         = 0.01
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   niter                          = 20
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   fcstep                         = 0
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   nstcgsteep                     = 200
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   nbfgscorr                      = 10
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   rtpi                           = 0.05
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   nstxout                        = 10
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   nstvout                        = 10
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   nstfout                        = 10
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   nstlog                         = 0
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   nstcalcenergy                  = 10
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   nstenergy                      = 10
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   nstxout-compressed             = 0
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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                          = 1.046
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   coulombtype                    = Cut-off
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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                     = 1
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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                       = 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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   tcoupl                         = V-rescale
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   nsttcouple                     = 10
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = No
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   pcoupltype                     = Isotropic
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   nstpcouple                     = -1
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   tau-p                          = 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                   = false
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 3
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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                = Equal
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   disre-mixed                    = false
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   dr-fc                          = 200
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   dr-tau                         = 0
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   nstdisreout                    = 20
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   orire-fc                       = 0
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   orire-tau                      = 0
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   nstorireout                    = 20
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   free-energy                    = no
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   cos-acceleration               = 0
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   deform (3x3):
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      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   simulated-tempering            = false
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   swapcoords                     = no
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   userint1                       = 0
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   userint2                       = 0
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   userint3                       = 0
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   userint4                       = 0
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   userreal1                      = 0
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   userreal2                      = 0
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   userreal3                      = 0
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   userreal4                      = 0
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   applied-forces:
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     electric-field:
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       x:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       y:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       z:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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grpopts:
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   nrdf:        2537
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   ref-t:         300
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   tau-t:         0.1
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annealing:          No
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annealing-npoints:           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 rlist from 1.046 to 1.051 for non-bonded 4x2 atom kernels
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Changing nstlist from 10 to 50, rlist from 1.051 to 1.286
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Using 1 MPI thread
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Using 8 OpenMP threads 
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1 GPU selected for this run.
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Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
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  PP:0
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PP tasks will do (non-perturbed) short-ranged interactions on the GPU
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Pinning threads with an auto-selected logical core stride of 1
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System total charge: 0.000
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Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Coulomb -1e+00
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Generated table with 1143 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1143 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1143 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Using GPU 4x4 nonbonded short-range kernels
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Using a dual 4x2 pair-list setup updated with dynamic, rolling pruning:
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  outer list: updated every 50 steps, buffer 0.286 nm, rlist 1.286 nm
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  inner list: updated every  4 steps, buffer 0.019 nm, rlist 1.019 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 0.346 nm, rlist 1.346 nm
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  inner list: updated every  4 steps, buffer 0.025 nm, rlist 1.025 nm
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Using Lorentz-Berthelot Lennard-Jones combination rule
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Removing pbc first time
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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 and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
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LINCS: A Linear Constraint Solver for molecular simulations
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J. Comp. Chem. 18 (1997) pp. 1463-1472
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-------- -------- --- Thank You --- -------- --------
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The number of constraints is 484
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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: 1007 Atoms
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Constraining the starting coordinates (step 0)
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Constraining the coordinates at t0-dt (step 0)
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RMS relative constraint deviation after constraining: 7.29e-07
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Initial temperature: 305.424 K
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Started mdrun on rank 0 Mon Jun 10 23:46:41 2019
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           Step           Time
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              0        0.00000
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   Energies (kJ/mol)
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           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
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    8.49567e+02    2.38781e+03    1.86323e+03    1.57600e+02   -3.65167e+02
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          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR) Position Rest.
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    9.32330e+02    1.40818e+04   -1.09261e+03   -2.00354e+04    5.96811e-05
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      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
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   -1.22083e+03    3.19570e+03    1.97487e+03    1.97487e+03    3.02999e+02
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 Pressure (bar)   Constr. rmsd
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   -6.87667e+01    1.02829e-06
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           Step           Time
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             10        0.02000
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Writing checkpoint, step 10 at Mon Jun 10 23:46:41 2019
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   Energies (kJ/mol)
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           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
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    9.58721e+02    2.29668e+03    1.85409e+03    1.53329e+02   -3.93716e+02
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          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR) Position Rest.
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    8.96268e+02    1.41027e+04   -1.13006e+03   -1.99805e+04    9.25166e+00
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      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
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   -1.23317e+03    3.20385e+03    1.97068e+03    1.96817e+03    3.03772e+02
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 Pressure (bar)   Constr. rmsd
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   -7.89550e+00    1.08599e-06
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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 11 steps using 2 frames
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   Energies (kJ/mol)
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           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
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    9.04144e+02    2.34225e+03    1.85866e+03    1.55465e+02   -3.79441e+02
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          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR) Position Rest.
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    9.14299e+02    1.40923e+04   -1.11133e+03   -2.00080e+04    4.62586e+00
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      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
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   -1.22700e+03    3.19977e+03    1.97277e+03    1.97152e+03    3.03385e+02
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 Pressure (bar)   Constr. rmsd
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   -3.83311e+01    0.00000e+00
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   Total Virial (kJ/mol)
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    7.97700e+02   -1.67735e+01   -5.88908e+01
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   -1.67593e+01    1.45876e+03    4.68493e+01
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   -5.13903e+01   -4.49568e+01    2.11402e+03
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   Pressure (bar)
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    2.50920e+01    3.65013e+00    5.49980e+00
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    3.64874e+00   -3.97868e+01   -6.87132e+00
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    4.76306e+00    2.14635e+00   -1.00299e+02
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	M E G A - F L O P S   A C C O U N T I N G
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 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
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 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
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 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
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 V&F=Potential and force  V=Potential only  F=Force only
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 Computing:                               M-Number         M-Flops  % Flops
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-----------------------------------------------------------------------------
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 Pair Search distance check               0.050000           0.450     0.3
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 NxN RF Elec. + LJ [F]                    2.507760          95.295    67.6
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 NxN RF Elec. + LJ [V&F]                  0.557280          30.093    21.4
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 1,4 nonbonded interactions               0.029183           2.626     1.9
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 Shift-X                                  0.001007           0.006     0.0
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 Bonds                                    0.006017           0.355     0.3
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 Propers                                  0.025916           5.935     4.2
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 Impropers                                0.001870           0.389     0.3
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 Pos. Restr.                              0.002112           0.106     0.1
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 Virial                                   0.002104           0.038     0.0
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 Calc-Ekin                                0.004028           0.109     0.1
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 Lincs                                    0.006292           0.378     0.3
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 Lincs-Mat                                0.024050           0.096     0.1
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 Constraint-V                             0.011616           0.093     0.1
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 Constraint-Vir                           0.000968           0.023     0.0
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 CMAP                                     0.000682           1.159     0.8
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 Urey-Bradley                             0.020405           3.734     2.7
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-----------------------------------------------------------------------------
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 Total                                                     140.885   100.0
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-----------------------------------------------------------------------------
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     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
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On 1 MPI rank, each using 8 OpenMP threads
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 Computing:          Num   Num      Call    Wall time         Giga-Cycles
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                     Ranks Threads  Count      (s)         total sum    %
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-----------------------------------------------------------------------------
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 Neighbor search        1    8          1       0.001          0.012   3.3
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 Launch GPU ops.        1    8         11       0.004          0.071  20.1
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 Force                  1    8         11       0.002          0.034   9.5
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 Wait GPU NB local      1    8         11       0.001          0.021   5.9
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 NB X/F buffer ops.     1    8         21       0.001          0.019   5.3
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 Write traj.            1    8          2       0.011          0.168  47.2
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 Update                 1    8         11       0.000          0.005   1.4
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 Constraints            1    8         13       0.001          0.020   5.6
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 Rest                                           0.000          0.006   1.8
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-----------------------------------------------------------------------------
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 Total                                          0.022          0.356 100.0
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-----------------------------------------------------------------------------
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 GPU timings
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-----------------------------------------------------------------------------
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 Computing:                         Count  Wall t (s)      ms/step       %
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-----------------------------------------------------------------------------
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 Pair list H2D                          1       0.000        0.016     0.5
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 X / q H2D                             11       0.000        0.004     1.2
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 Nonbonded F kernel                     9       0.002        0.205    54.5
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 Nonbonded F+ene k.                     2       0.001        0.681    40.2
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 Pruning kernel                         1       0.000        0.068     2.0
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 F D2H                                 11       0.000        0.005     1.6
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-----------------------------------------------------------------------------
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 Total                                          0.003        0.308   100.0
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-----------------------------------------------------------------------------
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 *Dynamic pruning                       4       0.000        0.022     2.6
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-----------------------------------------------------------------------------
469

    
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Average per-step force GPU/CPU evaluation time ratio: 0.308 ms/0.194 ms = 1.586
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               Core t (s)   Wall t (s)        (%)
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       Time:        0.178        0.022      796.1
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                 (ns/day)    (hour/ns)
475
Performance:       85.019        0.282
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Finished mdrun on rank 0 Mon Jun 10 23:46:41 2019
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