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md-rdd-2.log

Mark Abraham, 03/09/2017 04:27 PM

 
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Log file opened on Thu Mar  9 16:26:30 2017
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Host: tcbl02.scilifelab.se  pid: 27510  rank ID: 0  number of ranks:  1
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           :-) GROMACS - gmx mdrun, 2016.3-dev-20170307-942b2dc4b (-:
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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) 2001-2015, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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GROMACS:      gmx mdrun, version 2016.3-dev-20170307-942b2dc4b
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Executable:   /home/marklocal/git/r2016/build-cmake-gcc-gpu-release/install/bin/gmx
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Data prefix:  /home/marklocal/git/r2016/build-cmake-gcc-gpu-release/install
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Working dir:  /home/marklocal/redmines/redmine-2125
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Command line:
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  gmx mdrun -s md -notunepme -pin on -ntmpi 2 -v -rdd 2.0
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GROMACS version:    2016.3-dev-20170307-942b2dc4b
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GIT SHA1 hash:      942b2dc4b2c9f8704002428345df3bf893d46253
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Branched from:      e5242964a563c81e91e04ceea94c141a1772c1d1 (1 newer local commits)
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Precision:          single
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Memory model:       64 bit
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MPI library:        thread_mpi
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
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GPU support:        CUDA
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SIMD instructions:  AVX_256
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FFT library:        fftw-3.3.6-pl1-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:           Tue Jun 28 14:49:02 CEST 2016
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Built by:           marklocal@tcbl02.scilifelab.se [CMAKE]
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Build OS/arch:      Linux 4.6.3-1-ARCH x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
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Build CPU family:   6   Model: 58   Stepping: 9
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Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt 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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C compiler:         /home/marklocal/progs/bin/gcc-4.9 GNU 4.9.3
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C compiler flags:    -mavx    -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:       /home/marklocal/progs/bin/g++-4.9 GNU 4.9.3
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C++ compiler flags:  -mavx    -std=c++0x  -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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CUDA compiler:      /opt/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44
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CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_30,code=compute_30;-use_fast_math;-D_FORCE_INLINES;;-Xcompiler;,-mavx,,,,,,-Wundef,-Wextra,-Wno-missing-field-initializers,-Wpointer-arith,-Wall,-Wno-unused-function,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,-Wno-array-bounds,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,-Wno-array-bounds,; 
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CUDA driver:        8.0
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CUDA runtime:       8.0
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Running on 1 node with total 4 cores, 8 logical cores, 2 compatible GPUs
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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 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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    SIMD instructions most likely to fit this hardware: AVX_256
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    SIMD instructions selected at GROMACS compile time: AVX_256
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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   4] [   1   5] [   2   6] [   3   7]
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    Numa nodes:
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      Node  0 (16779456512 bytes mem):   0   1   2   3   4   5   6   7
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      Latency:
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               0
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         0  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: 8388608 bytes, linesize 64 bytes, assoc. 16, shared 8 ways
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    PCI devices:
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      0000:01:00.0  Id: 10de:1183  Class: 0x0300  Numa: 0
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      0000:02:00.0  Id: 10de:1401  Class: 0x0300  Numa: 0
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      0000:03:00.0  Id: 10ec:8168  Class: 0x0200  Numa: 0
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      0000:00:1f.2  Id: 8086:1e02  Class: 0x0106  Numa: 0
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  GPU info:
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    Number of GPUs detected: 2
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    #0: NVIDIA GeForce GTX 960, compute cap.: 5.2, ECC:  no, stat: compatible
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    #1: NVIDIA GeForce GTX 660 Ti, 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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Changing nstlist from 20 to 40, rlist from 1.137 to 1.22
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Input Parameters:
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   integrator                     = md
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   tinit                          = 0
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   dt                             = 0.01
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   nsteps                         = 1000000000
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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                        = 2210354616
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   emtol                          = 10
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   emstep                         = 0.01
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   niter                          = 20
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   fcstep                         = 0
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   nstcgsteep                     = 1000
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   nbfgscorr                      = 10
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   rtpi                           = 0.05
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   nstxout                        = 0
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   nstvout                        = 0
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   nstfout                        = 0
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   nstlog                         = 100000
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   nstcalcenergy                  = 100
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   nstenergy                      = 1000
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   nstxout-compressed             = 100000
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
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   nstlist                        = 40
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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                          = 1.22
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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                       = 1.1
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   epsilon-r                      = 15
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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                           = 1.1
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.22
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   fourier-nx                     = 144
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   fourier-ny                     = 160
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   fourier-nz                     = 160
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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                     = 20
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = Parrinello-Rahman
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   pcoupltype                     = Semiisotropic
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   nstpcouple                     = 20
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   tau-p                          = 12
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   compressibility (3x3):
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      compressibility[    0]={ 3.00000e-04,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  3.00000e-04,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  3.00000e-04}
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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               = All
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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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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = No
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   disre-weighting                = Conservative
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   disre-mixed                    = false
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   dr-fc                          = 1000
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   dr-tau                         = 0
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   nstdisreout                    = 100
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   orire-fc                       = 0
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   orire-tau                      = 0
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   nstorireout                    = 100
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   free-energy                    = no
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   cos-acceleration               = 0
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   deform (3x3):
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      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   simulated-tempering            = false
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   E-x:
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      n = 0
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   E-xt:
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      n = 0
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   E-y:
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      n = 0
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   E-yt:
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      n = 0
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   E-z:
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      n = 0
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   E-zt:
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      n = 0
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   swapcoords                     = no
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   userint1                       = 0
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   userint2                       = 0
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   userint3                       = 0
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   userint4                       = 0
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   userreal1                      = 0
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   userreal2                      = 0
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   userreal3                      = 0
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   userreal4                      = 0
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grpopts:
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   nrdf:      449086     3047.99      164021
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   ref-t:         310         310         310
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   tau-t:           1           1           1
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annealing:          No          No          No
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annealing-npoints:           0           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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Initializing Domain Decomposition on 2 ranks
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Dynamic load balancing: auto
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Minimum cell size due to bonded interactions: 2.000 nm
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Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 1.036 nm
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Estimated maximum distance required for P-LINCS: 1.036 nm
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Using 0 separate PME ranks, per user request
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Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
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Optimizing the DD grid for 2 cells with a minimum initial size of 2.500 nm
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The maximum allowed number of cells is: X 10 Y 10 Z 11
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Domain decomposition grid 2 x 1 x 1, separate PME ranks 0
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PME domain decomposition: 2 x 1 x 1
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Domain decomposition rank 0, coordinates 0 0 0
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The initial number of communication pulses is: X 1
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The initial domain decomposition cell size is: X 12.79 nm
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.220 nm
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(the following are initial values, they could change due to box deformation)
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            two-body bonded interactions  (-rdd)   2.000 nm
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          multi-body bonded interactions  (-rdd)   2.000 nm
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  atoms separated by up to 5 constraints  (-rcon) 12.792 nm
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When dynamic load balancing gets turned on, these settings will change to:
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The maximum number of communication pulses is: X 1
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The minimum size for domain decomposition cells is 2.000 nm
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The requested allowed shrink of DD cells (option -dds) is: 0.80
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The allowed shrink of domain decomposition cells is: X 0.16
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.220 nm
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            two-body bonded interactions  (-rdd)   2.000 nm
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          multi-body bonded interactions  (-rdd)   2.000 nm
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  atoms separated by up to 5 constraints  (-rcon)  2.000 nm
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Using 2 MPI threads
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Using 4 OpenMP threads per tMPI thread
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2 compatible GPUs are present, with IDs 0,1
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2 GPUs auto-selected for this run.
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Mapping of GPU IDs to the 2 PP ranks in this node: 0,1
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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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Will do ordinary reciprocal space Ewald sum.
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Using a Gaussian width (1/beta) of 0.352179 nm for Ewald
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Cut-off's:   NS: 1.22   Coulomb: 1.1   LJ: 1.1
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System total charge: 0.000
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Potential shift: LJ r^-12: -3.186e-01 r^-6: -5.645e-01, Ewald -1.000e-05
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Initialized non-bonded Ewald correction tables, spacing: 9.79e-04 size: 1126
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Using GPU 8x8 non-bonded kernels
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Using full Lennard-Jones parameter combination matrix
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Removing pbc first time
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Pinning threads with an auto-selected logical core stride of 1
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Initializing Parallel LINear Constraint Solver
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess
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P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 116-122
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-------- -------- --- Thank You --- -------- --------
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The number of constraints is 672
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There are inter charge-group constraints,
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will communicate selected coordinates each lincs iteration
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288 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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Linking all bonded interactions to atoms
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Intra-simulation communication will occur every 20 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: 205610 Atoms
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Atom distribution over 2 domains: av 102805 stddev 926 min 101879 max 103731
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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: 4.30e-06
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Initial temperature: 310.48 K
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Started mdrun on rank 0 Thu Mar  9 16:26:33 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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           Bond          Angle       G96Angle    Proper Dih.  Improper Dih.
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    8.88957e+04    1.00164e+03    4.26538e+04    2.56100e+02    1.04702e+03
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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   -5.03452e+06   -1.12943e+05    5.38024e+04   -4.95980e+06    7.96861e+05
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   Total Energy    Temperature Pressure (bar)   Constr. rmsd
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   -4.16294e+06    3.11092e+02    1.65967e+01    4.56214e-06
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DD  step 39 load imb.: force 20.7%
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Step 41  Warning: Pressure scaling more than 1%. This may mean your system
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 is not yet equilibrated. Use of Parrinello-Rahman pressure coupling during
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equilibration can lead to simulation instability, and is discouraged.
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-------------------------------------------------------
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Program:     gmx mdrun, version 2016.3-dev-20170307-942b2dc4b
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Source file: src/gromacs/ewald/pme-redistribute.cpp (line 282)
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MPI rank:    0 (out of 2)
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Fatal error:
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1 particles communicated to PME rank 0 are more than 2/3 times the cut-off out
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of the domain decomposition cell of their charge group in dimension x.
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This usually means that your system is not well equilibrated.
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For more information and tips for troubleshooting, please check the GROMACS
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website at http://www.gromacs.org/Documentation/Errors
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-------------------------------------------------------