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md-no-rdd.log

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

 
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Log file opened on Thu Mar  9 16:25:28 2017
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Host: tcbl02.scilifelab.se  pid: 27460  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
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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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Initial maximum inter charge-group distances:
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    two-body bonded interactions: 1.069 nm, Bond, atoms 24451 24638
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  multi-body bonded interactions: 1.153 nm, G96Angle, atoms 12306 12308
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Minimum cell size due to bonded interactions: 1.220 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 1.525 nm
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The maximum allowed number of cells is: X 16 Y 16 Z 18
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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)   1.220 nm
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          multi-body bonded interactions  (-rdd)   1.220 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 1.220 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 0.10
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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)   1.220 nm
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          multi-body bonded interactions  (-rdd)   1.220 nm
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  atoms separated by up to 5 constraints  (-rcon)  1.220 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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Not all bonded interactions have been properly assigned to the domain decomposition cells
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A list of missing interactions:
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                Bond of  76278 missing    163
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            G96Angle of  38248 missing    114
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         Proper Dih. of    552 missing      1
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       Improper Dih. of    744 missing      2
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Molecule type 'DOPE'
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the first 10 missing interactions, except for exclusions:
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            G96Angle atoms    2    3    5      global   242   243   245
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            G96Angle atoms    9   10   11      global   585   586   587
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            G96Angle atoms    5    6    7      global   725   726   727
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            G96Angle atoms    5    6    7      global   869   870   871
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            G96Angle atoms    2    3    5      global   890   891   893
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            G96Angle atoms    9   10   11      global   981   982   983
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            G96Angle atoms    3    5    6      global  1371  1373  1374
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            G96Angle atoms    4    9   10      global  1372  1377  1378
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            G96Angle atoms    5    6    7      global  1445  1446  1447
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            G96Angle atoms    5    6    7      global  1589  1590  1591
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            G96Angle atoms    3    5    6      global  1827  1829  1830
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            G96Angle atoms    2    3    5      global  2174  2175  2177
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            G96Angle atoms    2    3    4      global  2222  2223  2224
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                Bond atoms    1    2           global  2401  2402
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            G96Angle atoms    6    7    8      global  2706  2707  2708
447
            G96Angle atoms    3    5    6      global  2943  2945  2946
448
            G96Angle atoms    5    6    7      global  3833  3834  3835
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            G96Angle atoms    3    5    6      global  3939  3941  3942
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            G96Angle atoms    3    5    6      global  4215  4217  4218
451
            G96Angle atoms    6    7    8      global  4386  4387  4388
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            G96Angle atoms    2    3    5      global  4598  4599  4601
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            G96Angle atoms    6    7    8      global  4614  4615  4616
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            G96Angle atoms    9   10   11      global  4689  4690  4691
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            G96Angle atoms    6    7    8      global  4698  4699  4700
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            G96Angle atoms    2    3    5      global  5078  5079  5081
457
            G96Angle atoms    5    6    7      global  5261  5262  5263
458
            G96Angle atoms    3    5    6      global  5451  5453  5454
459
            G96Angle atoms    5    6    7      global  5573  5574  5575
460
            G96Angle atoms    2    3    4      global  5858  5859  5860
461
            G96Angle atoms    2    3    4      global  6158  6159  6160
462
            G96Angle atoms    2    3    5      global  6590  6591  6593
463
            G96Angle atoms    3    5    6      global  7443  7445  7446
464
            G96Angle atoms    3    5    6      global  7755  7757  7758
465
            G96Angle atoms    5    6    7      global  8705  8706  8707
466
            G96Angle atoms    9   10   11      global  8745  8746  8747
467
            G96Angle atoms    6    7    8      global  8982  8983  8984
468
            G96Angle atoms   10   11   12      global 10570 10571 10572
469
            G96Angle atoms    4    9   10      global 10720 10725 10726
470
            G96Angle atoms    5    6    7      global 10949 10950 10951
471
            G96Angle atoms    4    9   10      global 11152 11157 11158
472
            G96Angle atoms    2    3    4      global 11582 11583 11584
473
                Bond atoms    1    2           global 12337 12338
474
            G96Angle atoms    4    9   10      global 12952 12957 12958
475
            G96Angle atoms    6    7    8      global 12966 12967 12968
476
            G96Angle atoms    5    6    7      global 13433 13434 13435
477
            G96Angle atoms   10   11   12      global 13618 13619 13620
478
            G96Angle atoms    9   10   11      global 13701 13702 13703
479
            G96Angle atoms    6    7    8      global 13722 13723 13724
480
            G96Angle atoms    9   10   11      global 14085 14086 14087
481
            G96Angle atoms    5    6    7      global 14213 14214 14215
482
            G96Angle atoms    9   10   11      global 14625 14626 14627
483
            G96Angle atoms    6    7    8      global 15270 15271 15272
484
            G96Angle atoms    4    9   10      global 15376 15381 15382
485
            G96Angle atoms    5    6    7      global 15449 15450 15451
486
            G96Angle atoms    4    9   10      global 15544 15549 15550
487
            G96Angle atoms   10   11   12      global 16150 16151 16152
488
            G96Angle atoms    2    3    4      global 16622 16623 16624
489
            G96Angle atoms    9   10   11      global 16821 16822 16823
490
            G96Angle atoms    6    7    8      global 17010 17011 17012
491
            G96Angle atoms    2    3    5      global 17186 17187 17189
492
            G96Angle atoms    3    5    6      global 17199 17201 17202
493
            G96Angle atoms    6    7    8      global 17298 17299 17300
494
            G96Angle atoms    2    3    5      global 17390 17391 17393
495
            G96Angle atoms    3    5    6      global 17415 17417 17418
496
            G96Angle atoms    5    6    7      global 17693 17694 17695
497
            G96Angle atoms    9   10   11      global 17841 17842 17843
498
                Bond atoms    1    2           global 17929 17930
499
            G96Angle atoms    9   10   11      global 18129 18130 18131
500
            G96Angle atoms    5    6    7      global 18245 18246 18247
501
            G96Angle atoms    4    9   10      global 18364 18369 18370
502
            G96Angle atoms   10   11   12      global 18574 18575 18576
503
            G96Angle atoms    5    6    7      global 18701 18702 18703
504

    
505
Molecule type 'DOTAP'
506
the first 10 missing interactions, except for exclusions:
507
            G96Angle atoms    1    2    4      global 19939 19940 19942
508
            G96Angle atoms    2    4    5      global 20699 20701 20702
509
            G96Angle atoms    5    6    7      global 21318 21319 21320
510
            G96Angle atoms    4    5    6      global 21834 21835 21836
511
                Bond atoms    5    6           global 21835 21836
512
            G96Angle atoms    5    6    7      global 21835 21836 21837
513
            G96Angle atoms    3    8    9      global 21910 21915 21916
514
                Bond atoms    8    9           global 21915 21916
515
            G96Angle atoms    8    9   10      global 21915 21916 21917
516
            G96Angle atoms    5    6    7      global 22451 22452 22453
517
            G96Angle atoms    1    2    3      global 22733 22734 22735
518
            G96Angle atoms    9   10   11      global 22763 22764 22765
519
            G96Angle atoms    1    2    3      global 23085 23086 23087
520
            G96Angle atoms    9   10   11      global 23797 23798 23799
521
            G96Angle atoms    5    6    7      global 23815 23816 23817
522
            G96Angle atoms    3    8    9      global 24033 24038 24039
523

    
524
Molecule type 'Nucleic_A+Nucleic_B'
525
the first 10 missing interactions, except for exclusions:
526
                Bond atoms   49   62           global 24433 24446
527
                Bond atoms   49  251           global 24433 24635
528
                Bond atoms   50   62           global 24434 24446
529
                Bond atoms   50  250           global 24434 24634
530
                Bond atoms   50  251           global 24434 24635
531
                Bond atoms   51   62           global 24435 24446
532
                Bond atoms   51  249           global 24435 24633
533
                Bond atoms   51  250           global 24435 24634
534
                Bond atoms   51  251           global 24435 24635
535
                Bond atoms   53   62           global 24437 24446
536
                Bond atoms   31   45           global 25035 25049
537

    
538
-------------------------------------------------------
539
Program:     gmx mdrun, version 2016.3-dev-20170307-942b2dc4b
540
Source file: src/gromacs/domdec/domdec_topology.cpp (line 434)
541
MPI rank:    0 (out of 2)
542

    
543
Fatal error:
544
280 of the 116686 bonded interactions could not be calculated because some
545
atoms involved moved further apart than the multi-body cut-off distance (1.22
546
nm) or the two-body cut-off distance (1.22 nm), see option -rdd, for pairs and
547
tabulated bonds also see option -ddcheck
548

    
549
For more information and tips for troubleshooting, please check the GROMACS
550
website at http://www.gromacs.org/Documentation/Errors
551
-------------------------------------------------------