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automation_with_extra_info.log

Szilárd Páll, 07/16/2015 12:18 AM

 
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Log file opened on Wed Jul 15 13:09:49 2015
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Host: SC-HPC-013  pid: 15075  rank ID: 0  number of ranks:  1
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                  :-) GROMACS - gmx mdrun, VERSION 5.1-rc1 (-:
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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   Sebastian Fritsch 
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  Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen
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 Dimitrios Karkoulis    Peter Kasson     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 5.1-rc1
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Executable:   /var/data0/sandbox/gromacs/bmdir/data/gromacs-runnable/bin/gmx
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Data prefix:  /var/data0/sandbox/gromacs/bmdir/data/gromacs-runnable
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Command line:
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  gmx mdrun -nb gpu -nsteps 1000 -resethway -noconfout -v -ntomp 6 -ntmpi 2
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GROMACS version:    VERSION 5.1-rc1
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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:        enabled
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OpenCL support:     disabled
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invsqrt routine:    gmx_software_invsqrt(x)
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SIMD instructions:  AVX_256
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FFT library:        fftw-3.3.4-sse2-avx
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RDTSCP usage:       enabled
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C++11 compilation:  disabled
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TNG support:        enabled
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Tracing support:    disabled
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Built on:           Wed Jul 15 12:43:12 PDT 2015
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Built by:           root@SC-HPC-013 [CMAKE]
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Build OS/arch:      Linux 2.6.32-504.el6.x86_64 x86_64
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Build CPU vendor:   GenuineIntel
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Build CPU brand:    Intel(R) Xeon(R) CPU E5-2697 v2 @ 2.70GHz
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Build CPU family:   6   Model: 62   Stepping: 4
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Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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C compiler:         /opt/rh/devtoolset-2/root/usr/bin/gcc GNU 4.8.2
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C compiler flags:    -mavx    -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:       /opt/rh/devtoolset-2/root/usr/bin/g++ GNU 4.8.2
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C++ compiler flags:  -mavx    -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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Boost version:      1.55.0 (internal)
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CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2014 NVIDIA Corporation;Built on Wed_Aug_27_10:36:36_CDT_2014;Cuda compilation tools, release 6.5, V6.5.16
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CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_50,code=compute_50;-use_fast_math;; ;-mavx;-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 driver:        7.0
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CUDA runtime:       6.50
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Number of logical cores detected (24) does not match the number reported by OpenMP (12).
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Consider setting the launch configuration manually!
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Running on 1 node with total 24 cores, 24 logical cores, 2 compatible GPUs
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Hardware detected:
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  CPU info:
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    Vendor: GenuineIntel
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    Brand:  Intel(R) Xeon(R) CPU E5-2697 v2 @ 2.70GHz
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    Family:  6  model: 62  stepping:  4
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    CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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    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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  GPU info:
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    Number of GPUs detected: 2
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    #0: NVIDIA Tesla K40c, compute cap.: 3.5, ECC:  no, stat: compatible
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    #1: NVIDIA Tesla K40c, compute cap.: 3.5, ECC:  no, stat: compatible
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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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For optimal performance with a GPU nstlist (now 10) should be larger.
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The optimum depends on your CPU and GPU resources.
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You might want to try several nstlist values.
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Changing nstlist from 10 to 40, rlist from 1 to 1.101
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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                         = 250
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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                        = 2881701017
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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                         = 0
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   nstcalcenergy                  = 100
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   nstenergy                      = 0
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   nstxout-compressed             = 0
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
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   nstlist                        = 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                          = 1.101
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   rlistlong                      = 1.101
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   nstcalclr                      = 10
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   coulombtype                    = PME
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   coulomb-modifier               = Potential-shift
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   rcoulomb-switch                = 0
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   rcoulomb                       = 1
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   epsilon-r                      = 1
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   epsilon-rf                     = inf
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   vdw-type                       = Cut-off
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   vdw-modifier                   = Potential-shift
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   rvdw-switch                    = 0
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   rvdw                           = 1
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.125
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   fourier-nx                     = 200
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   fourier-ny                     = 100
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   fourier-nz                     = 100
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   pme-order                      = 4
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   ewald-rtol                     = 1e-05
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   ewald-rtol-lj                  = 0.001
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   lj-pme-comb-rule               = Geometric
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   ewald-geometry                 = 0
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   epsilon-surface                = 0
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   implicit-solvent               = No
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   gb-algorithm                   = Still
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   nstgbradii                     = 1
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   rgbradii                       = 1
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   gb-epsilon-solvent             = 80
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   gb-saltconc                    = 0
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   gb-obc-alpha                   = 1
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   gb-obc-beta                    = 0.8
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   gb-obc-gamma                   = 4.85
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   gb-dielectric-offset           = 0.009
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   sa-algorithm                   = Ace-approximation
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   sa-surface-tension             = 2.05016
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   tcoupl                         = V-rescale
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   nsttcouple                     = 10
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = FALSE
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   pcoupl                         = No
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   pcoupltype                     = Isotropic
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   nstpcouple                     = -1
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   tau-p                          = 1
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   compressibility (3x3):
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      compressibility[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   ref-p (3x3):
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      ref-p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   refcoord-scaling               = No
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   posres-com (3):
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      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = FALSE
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = FALSE
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   Shake-SOR                      = FALSE
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   shake-tol                      = 0.0001
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   lincs-order                    = 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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   adress                         = FALSE
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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:      767997
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   ref-t:         300
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   tau-t:         0.1
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annealing:          No
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annealing-npoints:           0
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   acc:	           0           0           0
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   nfreeze:           N           N           N
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   energygrp-flags[  0]: 0
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Overriding nsteps with value passed on the command line: 1000 steps, 2 ps
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Initializing Domain Decomposition on 2 ranks
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Dynamic load balancing: auto
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Will sort the charge groups at every domain (re)decomposition
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Minimum cell size due to bonded interactions: 0.000 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 0.126 nm
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The maximum allowed number of cells is: X 197 Y 98 Z 98
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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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Using 2 MPI threads
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Using 6 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 0.320163 nm for Ewald
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Cut-off's:   NS: 1.101   Coulomb: 1   LJ: 1
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System total charge: 0.000
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Generated table with 1050 data points for Ewald.
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Tabscale = 500 points/nm
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Generated table with 1050 data points for LJ6.
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Tabscale = 500 points/nm
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Generated table with 1050 data points for LJ12.
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Tabscale = 500 points/nm
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Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
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Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
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Note: NVML support was not found (CUDA runtime 6.50, driver 7.0), so your
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      Tesla K40c GPU cannot use application clock support to improve performance.
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Using GPU 8x8 non-bonded kernels
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Removing pbc first time
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NOTE: The number of threads is not equal to the number of (logical) cores
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      and the -pin option is set to auto: will not pin thread to cores.
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      This can lead to significant performance degradation.
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      Consider using -pin on (and -pinoffset in case you run multiple jobs).
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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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Linking all bonded interactions to atoms
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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 12.46 nm
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.101 nm
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            two-body bonded interactions  (-rdd)   1.101 nm
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          multi-body bonded interactions  (-rdd)   1.101 nm
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  atoms separated by up to 5 constraints  (-rcon) 12.459 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 1.101 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 0.09
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.101 nm
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            two-body bonded interactions  (-rdd)   1.101 nm
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          multi-body bonded interactions  (-rdd)   1.101 nm
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  atoms separated by up to 5 constraints  (-rcon)  1.101 nm
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Making 1D domain decomposition grid 2 x 1 x 1, home cell index 0 0 0
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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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