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test-1.log

mdrun log file for run that works ok. - Eiso AB, 05/15/2019 09:02 AM

 
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Log file opened on Tue May 14 23:46:15 2019
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Host: zeepoes  pid: 30855  rank ID: 0  number of ranks:  1
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                    :-) GROMACS - gmx mdrun, 2019-beta1 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
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    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  
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  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   
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 Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    
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  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  
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  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   
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    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  
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   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen 
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 Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2017, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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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-beta1
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Executable:   /usr/local/gromacs/bin/gmx
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Data prefix:  /usr/local/gromacs
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Working dir:  /home/eiso/gmx-test/ORIG
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Command line:
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  gmx mdrun -v -deffnm test -c test.pdb
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GROMACS version:    2019-beta1
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Precision:          single
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Memory model:       64 bit
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MPI library:        thread_mpi
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support:        CUDA
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SIMD instructions:  AVX_256
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FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      disabled
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Tracing support:    disabled
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C compiler:         /usr/bin/cc GNU 4.8.5
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C compiler flags:    -mavx     -O2 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /usr/bin/c++ GNU 4.8.5
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C++ compiler flags:  -mavx    -std=c++11   -O2 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Fri_Feb__8_19:08:17_PST_2019;Cuda compilation tools, release 10.1, V10.1.105
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CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;;; ;-mavx;-std=c++11;-O2;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
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CUDA driver:        10.10
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CUDA runtime:       10.10
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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) i7-3770 CPU @ 3.40GHz
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    Family: 6   Model: 58   Stepping: 9
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    Features: aes apic avx clfsh cmov cx8 cx16 f16c htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm 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: NVIDIA GeForce GT 640, compute cap.: 3.0, ECC:  no, 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                         = 50000
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   init-step                      = 0
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   simulation-part                = 1
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   comm-mode                      = Linear
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   nstcomm                        = 100
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   bd-fric                        = 0
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   ld-seed                        = 1993
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   emtol                          = 100
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   emstep                         = 0.01
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   niter                          = 20
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   fcstep                         = 0
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   nstcgsteep                     = 1000
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   nbfgscorr                      = 10
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   rtpi                           = 0.05
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   nstxout                        = 0
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   nstvout                        = 0
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   nstfout                        = 0
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   nstlog                         = 5000
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   nstcalcenergy                  = 100
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   nstenergy                      = 0
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   nstxout-compressed             = 500
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
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   nstlist                        = 10
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   ns-type                        = Grid
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   pbc                            = xyz
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   periodic-molecules             = false
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   verlet-buffer-tolerance        = 0.005
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   rlist                          = 0.969
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   coulombtype                    = Reaction-Field
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   coulomb-modifier               = Potential-shift
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   rcoulomb-switch                = 0
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   rcoulomb                       = 0.9
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   epsilon-r                      = 1
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   epsilon-rf                     = inf
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   vdw-type                       = Cut-off
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   vdw-modifier                   = Potential-shift
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   rvdw-switch                    = 0
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   rvdw                           = 0.9
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.12
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   fourier-nx                     = 28
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   fourier-ny                     = 28
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   fourier-nz                     = 28
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   pme-order                      = 4
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   ewald-rtol                     = 1e-05
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   ewald-rtol-lj                  = 0.001
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   lj-pme-comb-rule               = Geometric
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   ewald-geometry                 = 0
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   epsilon-surface                = 0
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   tcoupl                         = V-rescale
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   nsttcouple                     = 10
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = No
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   pcoupltype                     = Isotropic
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   nstpcouple                     = -1
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   tau-p                          = 2
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   compressibility (3x3):
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      compressibility[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   ref-p (3x3):
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      ref-p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   refcoord-scaling               = No
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   posres-com (3):
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      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = false
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = false
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 4
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   lincs-iter                     = 1
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   lincs-warnangle                = 30
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   nwall                          = 0
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   wall-type                      = 9-3
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   wall-r-linpot                  = -1
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   wall-atomtype[0]               = -1
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   wall-atomtype[1]               = -1
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   wall-density[0]                = 0
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   wall-density[1]                = 0
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   wall-ewald-zfac                = 3
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   pull                           = false
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   awh                            = false
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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = Simple
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   disre-weighting                = Conservative
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   disre-mixed                    = false
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   dr-fc                          = 1000
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   dr-tau                         = 0
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   nstdisreout                    = 100
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   orire-fc                       = 0
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   orire-tau                      = 0
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   nstorireout                    = 100
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   free-energy                    = no
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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:        2397
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   ref-t:         298
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   tau-t:         0.5
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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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Initializing the distance restraints
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There are 1 distance restraints involving 1 atom pairs
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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J. Tropp
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Dipolar Relaxation and Nuclear Overhauser effects in nonrigid molecules: The
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effect of fluctuating internuclear distances
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J. Chem. Phys. 72 (1980) pp. 6035-6043
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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A. E. Torda and R. M. Scheek and W. F. van Gunsteren
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Time-dependent distance restraints in molecular dynamics simulations
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Chem. Phys. Lett. 157 (1989) pp. 289-294
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-------- -------- --- Thank You --- -------- --------
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Changing nstlist from 10 to 25, rlist from 0.969 to 1.126
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Using 1 MPI thread
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Using 8 OpenMP threads 
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1 GPU auto-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 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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Reaction-Field:
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epsRF = 0, rc = 0.9, krf = 0.685871, crf = 1.66667, epsfac = 138.935
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The electrostatics potential has its minimum at r = 0.9
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Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00
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Using GPU 8x8 nonbonded short-range kernels
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Using a dual 8x4 pair-list setup updated with dynamic, rolling pruning:
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  outer list: updated every 25 steps, buffer 0.226 nm, rlist 1.126 nm
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  inner list: updated every  4 steps, buffer 0.023 nm, rlist 0.923 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 25 steps, buffer 0.286 nm, rlist 1.186 nm
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  inner list: updated every  4 steps, buffer 0.035 nm, rlist 0.935 nm
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Using geometric Lennard-Jones combination rule
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Removing pbc first time
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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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 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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++++ 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: 1200 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: 0.00e+00
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Initial temperature: 295.783 K
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Started mdrun on rank 0 Tue May 14 23:46:15 2019
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           Step           Time
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              0        0.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.94214e+03   -2.25672e+04    3.75567e+02    8.66679e-01   -1.82495e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
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    2.99265e+03   -1.52568e+04   -1.52568e+04    3.00320e+02    5.12250e+02
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           Step           Time
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           5000       10.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.93590e+03   -2.27340e+04    1.01413e+00    4.50363e-02   -1.87971e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
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    2.95568e+03   -1.58414e+04   -1.55386e+04    2.96609e+02    3.55413e+02
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           Step           Time
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          10000       20.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.69277e+03   -2.23121e+04    4.62344e+00    9.61607e-02   -1.86147e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
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    2.99488e+03   -1.56198e+04   -1.55264e+04    3.00543e+02   -4.21211e+02
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           Step           Time
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          15000       30.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.66814e+03   -2.24271e+04    1.16076e-01    1.52365e-02   -1.87588e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
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    2.99141e+03   -1.57674e+04   -1.55116e+04    3.00195e+02   -6.54210e+02
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           Step           Time
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          20000       40.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.68193e+03   -2.21672e+04    1.78874e-01    1.89142e-02   -1.84851e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
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    2.85946e+03   -1.56256e+04   -1.54965e+04    2.86954e+02    5.84505e+01
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           Step           Time
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          25000       50.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.70222e+03   -2.25150e+04    4.83795e-01    3.11061e-02   -1.88123e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
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    2.96824e+03   -1.58441e+04   -1.54851e+04    2.97870e+02   -4.44626e+02
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           Step           Time
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          30000       60.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.72751e+03   -2.25236e+04    8.62260e-01    4.15273e-02   -1.87952e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
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    2.83621e+03   -1.59590e+04   -1.54710e+04    2.84620e+02   -4.29100e+02
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           Step           Time
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          35000       70.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.80111e+03   -2.23204e+04    1.59768e-01    1.78756e-02   -1.85191e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
430
    3.04929e+03   -1.54698e+04   -1.54596e+04    3.06004e+02    6.56170e+02
431

    
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           Step           Time
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          40000       80.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.74549e+03   -2.23316e+04    3.31397e-02    8.14122e-03   -1.85860e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
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    3.03539e+03   -1.55507e+04   -1.54465e+04    3.04608e+02    9.02513e+01
440

    
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           Step           Time
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          45000       90.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.64893e+03   -2.22756e+04    4.50653e+00    9.49372e-02   -1.86222e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
448
    2.91995e+03   -1.57022e+04   -1.54344e+04    2.93024e+02   -1.86476e+00
449

    
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           Step           Time
451
          50000      100.00000
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Writing checkpoint, step 50000 at Tue May 14 23:46:32 2019
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
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    3.62471e+03   -2.23559e+04    1.04439e+00    4.57032e-02   -1.87301e+04
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
460
    2.96976e+03   -1.57604e+04   -1.54192e+04    2.98023e+02   -9.24147e+02
461

    
462
	<======  ###############  ==>
463
	<====  A V E R A G E S  ====>
464
	<==  ###############  ======>
465

    
466
	Statistics over 50001 steps using 501 frames
467

    
468
   Energies (kJ/mol)
469
        LJ (SR)   Coulomb (SR)     Dis. Rest. D.R.Viol. (nm)      Potential
470
    3.79117e+03   -2.24542e+04    9.05956e+00    6.30235e-02   -1.86540e+04
471
    Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
472
    2.98220e+03   -1.56718e+04   -1.54797e+04    2.99271e+02    9.33625e+01
473

    
474
   Total Virial (kJ/mol)
475
    9.68025e+02   -7.37505e+00   -1.22947e+01
476
   -7.35718e+00    9.54344e+02    3.00760e-01
477
   -1.23066e+01    2.94330e-01    9.58111e+02
478

    
479
   Pressure (bar)
480
    6.72176e+01    2.24448e+01    3.10723e+01
481
    2.23956e+01    1.08355e+02    1.94874e+00
482
    3.11051e+01    1.96644e+00    1.04515e+02
483

    
484

    
485
	M E G A - F L O P S   A C C O U N T I N G
486

    
487
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
488
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
489
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
490
 V&F=Potential and force  V=Potential only  F=Force only
491

    
492
 Computing:                               M-Number         M-Flops  % Flops
493
-----------------------------------------------------------------------------
494
 Pair Search distance check             158.376320        1425.387     0.1
495
 NxN RF Elec. + LJ [F]                55587.393088     2112320.937    98.2
496
 NxN RF Elec. + LJ [V&F]                562.541376       30377.234     1.4
497
 Shift-X                                  2.401200          14.407     0.0
498
 Dist. Restr.                             0.050001          10.000     0.0
499
 Virial                                   0.623745          11.227     0.0
500
 Stop-CM                                  0.602400           6.024     0.0
501
 Calc-Ekin                               24.002400         648.065     0.0
502
 Constraint-V                            60.002400         480.019     0.0
503
 Constraint-Vir                           0.601200          14.429     0.0
504
 Settle                                  20.001200        6460.388     0.3
505
-----------------------------------------------------------------------------
506
 Total                                                 2151768.118   100.0
507
-----------------------------------------------------------------------------
508

    
509

    
510
     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
511

    
512
On 1 MPI rank, each using 8 OpenMP threads
513

    
514
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
515
                     Ranks Threads  Count      (s)         total sum    %
516
-----------------------------------------------------------------------------
517
 Neighbor search        1    8       2001       0.469         12.714   2.7
518
 Launch GPU ops.        1    8      50001       1.755         47.626  10.2
519
 Force                  1    8      50001       0.633         17.189   3.7
520
 Wait GPU NB local      1    8      50001      11.597        314.724  67.3
521
 NB X/F buffer ops.     1    8      98001       1.179         32.006   6.8
522
 Write traj.            1    8        101       0.037          1.002   0.2
523
 Update                 1    8      50001       0.504         13.689   2.9
524
 Constraints            1    8      50003       0.546         14.831   3.2
525
 Rest                                           0.507         13.755   2.9
526
-----------------------------------------------------------------------------
527
 Total                                         17.228        467.538 100.0
528
-----------------------------------------------------------------------------
529

    
530
               Core t (s)   Wall t (s)        (%)
531
       Time:      137.823       17.228      800.0
532
                 (ns/day)    (hour/ns)
533
Performance:      501.519        0.048
534
Finished mdrun on rank 0 Tue May 14 23:46:32 2019
535