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md.log

Siyoung Kim, 08/14/2019 03:27 AM

 
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Log file opened on Tue Aug 13 20:16:00 2019
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Host: midway2-0652.rcc.local  pid: 49952  rank ID: 0  number of ranks:  4
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                      :-) GROMACS - gmx mdrun, 2018.3 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
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    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  
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  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   
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 Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    
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  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  
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  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   
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    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  
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   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen 
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 Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2017, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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GROMACS:      gmx mdrun, version 2018.3
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Executable:   /home/siyoungkim/software/gromacs-2018.3/install/bin/gmx
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Data prefix:  /home/siyoungkim/software/gromacs-2018.3/install
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Working dir:  /project/gavoth/siyoungkim/TG/01/performance_test/04
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Command line:
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  gmx mdrun -deffnm md -v -ntomp 10 -nb gpu -pme gpu -npme 1 -gputasks 0123 -nsteps 1000000
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GROMACS version:    2018.3
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Precision:          single
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Memory model:       64 bit
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MPI library:        MPI
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support:        CUDA
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SIMD instructions:  AVX2_256
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FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      hwloc-1.11.2
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Tracing support:    disabled
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Built on:           2019-08-13 22:37:36
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Built by:           siyoungkim@midway2-login2.rcc.local [CMAKE]
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Build OS/arch:      Linux 3.10.0-957.12.2.el7.x86_64 x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
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Build CPU family:   6   Model: 79   Stepping: 1
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Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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C compiler:         /bin/cc GNU 4.8.5
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C compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /bin/c++ GNU 4.8.5
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C++ compiler flags:  -march=core-avx2    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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CUDA compiler:      /software/cuda-10.0-el7-x86_64/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on Sat_Aug_25_21:08:01_CDT_2018;Cuda compilation tools, release 10.0, V10.0.130
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CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;;; ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
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CUDA driver:        10.10
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CUDA runtime:       10.0
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Note: 80 CPUs configured, but only 40 were detected to be online.
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      X86 Hyperthreading is likely disabled; enable it for better performance.
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Running on 1 node with total 40 cores, 40 logical cores, 4 compatible GPUs
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Hardware detected on host midway2-0652.rcc.local (the node of MPI rank 0):
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  CPU info:
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    Vendor: Intel
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    Brand:  Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
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    Family: 6   Model: 85   Stepping: 4
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    Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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    Number of AVX-512 FMA units: Cannot run AVX-512 detection - assuming 2
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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] [   1] [   2] [   3] [   4] [   5] [   6] [   7] [   8] [   9] [  10] [  11] [  12] [  13] [  14] [  15] [  16] [  17] [  18] [  19]
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      Socket  1: [  20] [  21] [  22] [  23] [  24] [  25] [  26] [  27] [  28] [  29] [  30] [  31] [  32] [  33] [  34] [  35] [  36] [  37] [  38] [  39]
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    Numa nodes:
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      Node  0 (102741385216 bytes mem):   0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19
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      Node  1 (103079215104 bytes mem):  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39
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      Latency:
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               0     1
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         0  1.00  2.10
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         1  2.10  1.00
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    Caches:
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      L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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      L2: 1048576 bytes, linesize 64 bytes, assoc. 16, shared 1 ways
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      L3: 28835840 bytes, linesize 64 bytes, assoc. 11, shared 20 ways
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    PCI devices:
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      0000:00:17.0  Id: 8086:2826  Class: 0x0104  Numa: 0
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      0000:02:00.0  Id: 102b:0522  Class: 0x0300  Numa: 0
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      0000:03:00.0  Id: 8086:1521  Class: 0x0200  Numa: 0
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      0000:03:00.1  Id: 8086:1521  Class: 0x0200  Numa: 0
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      0000:06:00.0  Id: 10de:1db4  Class: 0x0302  Numa: 0
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      0000:2f:00.0  Id: 10de:1db4  Class: 0x0302  Numa: 0
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      0000:58:00.0  Id: 15b3:1017  Class: 0x0207  Numa: 0
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      0000:58:00.1  Id: 15b3:1017  Class: 0x0207  Numa: 0
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      0000:86:00.0  Id: 10de:1db4  Class: 0x0302  Numa: 1
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      0000:d8:00.0  Id: 10de:1db4  Class: 0x0302  Numa: 1
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  GPU info:
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    Number of GPUs detected: 4
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    #0: NVIDIA Tesla V100-PCIE-16GB, compute cap.: 7.0, ECC: yes, stat: compatible
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    #1: NVIDIA Tesla V100-PCIE-16GB, compute cap.: 7.0, ECC: yes, stat: compatible
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    #2: NVIDIA Tesla V100-PCIE-16GB, compute cap.: 7.0, ECC: yes, stat: compatible
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    #3: NVIDIA Tesla V100-PCIE-16GB, compute cap.: 7.0, ECC: yes, stat: compatible
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Highest SIMD level requested by all nodes in run: AVX_512
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SIMD instructions selected at compile time:       AVX2_256
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This program was compiled for different hardware than you are running on,
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which could influence performance. This build might have been configured on a
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login node with only a single AVX-512 FMA unit (in which case AVX2 is faster),
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while the node you are running on has dual AVX-512 FMA units.
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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
127
GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
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GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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Input Parameters:
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   integrator                     = md
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   tinit                          = 0
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   dt                             = 0.002
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   nsteps                         = 500000000
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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                        = 2134866680
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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                         = 5000
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   nstcalcenergy                  = 100
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   nstenergy                      = 1000
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   nstxout-compressed             = 50000
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
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   nstlist                        = 20
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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                          = 1.2
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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                       = 1.2
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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                   = Force-switch
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   rvdw-switch                    = 1
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   rvdw                           = 1.2
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.12
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   fourier-nx                     = 240
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   fourier-ny                     = 240
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   fourier-nz                     = 864
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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                          = 5
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   compressibility (3x3):
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      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
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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               = COM
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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                   = true
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 4
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   lincs-iter                     = 1
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   lincs-warnangle                = 30
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   nwall                          = 0
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   wall-type                      = 9-3
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   wall-r-linpot                  = -1
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   wall-atomtype[0]               = -1
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   wall-atomtype[1]               = -1
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   wall-density[0]                = 0
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   wall-density[1]                = 0
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   wall-ewald-zfac                = 3
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   pull                           = false
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   awh                            = false
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   rotation                       = false
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   interactiveMD                  = false
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   disre                          = 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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   swapcoords                     = no
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   userint1                       = 0
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   userint2                       = 0
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   userint3                       = 0
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   userint4                       = 0
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   userreal1                      = 0
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   userreal2                      = 0
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   userreal3                      = 0
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   userreal4                      = 0
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   applied-forces:
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     electric-field:
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       x:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       y:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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       z:
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         E0                       = 0
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         omega                    = 0
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         t0                       = 0
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         sigma                    = 0
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grpopts:
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   nrdf:      897997      983589       11113
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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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The -nsteps functionality is deprecated, and may be removed in a future version. Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.
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Overriding nsteps with value passed on the command line: 1000000 steps, 2e+03 ps
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Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
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Initializing Domain Decomposition on 4 ranks
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Dynamic load balancing: locked
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Minimum cell size due to atom displacement: 0.821 nm
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Initial maximum inter charge-group distances:
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    two-body bonded interactions: 0.420 nm, LJ-14, atoms 322992 323001
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  multi-body bonded interactions: 0.420 nm, Proper Dih., atoms 322992 323001
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Minimum cell size due to bonded interactions: 0.462 nm
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Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm
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Estimated maximum distance required for P-LINCS: 0.222 nm
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Using 1 separate PME ranks
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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 3 cells with a minimum initial size of 1.026 nm
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The maximum allowed number of cells is: X 27 Y 27 Z 97
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Domain decomposition grid 1 x 1 x 3, separate PME ranks 1
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PME domain decomposition: 1 x 1 x 1
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Interleaving PP and PME ranks
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This rank does only particle-particle work.
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Domain decomposition rank 0, coordinates 0 0 0
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The initial number of communication pulses is: Z 1
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The initial domain decomposition cell size is: Z 33.40 nm
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.200 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)   1.200 nm
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          multi-body bonded interactions  (-rdd)   1.200 nm
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  atoms separated by up to 5 constraints  (-rcon) 28.291 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: Z 1
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The minimum size for domain decomposition cells is 1.200 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: Z 0.04
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.200 nm
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            two-body bonded interactions  (-rdd)   1.200 nm
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          multi-body bonded interactions  (-rdd)   1.200 nm
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  atoms separated by up to 5 constraints  (-rcon)  1.200 nm
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Using 4 MPI processes
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Using 10 OpenMP threads per MPI process
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On host midway2-0652.rcc.local 4 GPUs user-selected for this run.
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Mapping of GPU IDs to the 4 GPU tasks in the 4 ranks on this node:
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  PP:0,PP:1,PP:2,PME:3
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NOTE: Your choice of number of MPI ranks and amount of resources results in using 10 OpenMP threads per rank, which is most likely inefficient. The optimum is usually between 2 and 6 threads per rank.
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NOTE: GROMACS was configured without NVML support hence it can not exploit
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      application clocks of the detected Tesla V100-PCIE-16GB GPU to improve performance.
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      Recompile with the NVML library (compatible with the driver used) or set application clocks manually.
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Non-default thread affinity set probably by the OpenMP library,
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disabling internal thread affinity
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System total charge: 0.000
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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 ++++
407
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
408
A smooth particle mesh Ewald method
409
J. Chem. Phys. 103 (1995) pp. 8577-8592
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-------- -------- --- Thank You --- -------- --------
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Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
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Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06
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Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176
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Generated table with 1100 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1100 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1100 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Using GPU 8x8 nonbonded short-range kernels
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425
Using a 8x4 pair-list setup:
426
  updated every 100 steps, buffer 0.000 nm, rlist 1.200 nm
427
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
428
  updated every 100 steps, buffer 0.132 nm, rlist 1.332 nm
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431
Initializing Parallel LINear Constraint Solver
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433
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
434
B. Hess
435
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
436
J. Chem. Theory Comput. 4 (2008) pp. 116-122
437
-------- -------- --- Thank You --- -------- --------
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The number of constraints is 229312
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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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++++ 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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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:  MEMB
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  1:  SOL_ION
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  2:  TRIO
460

    
461
++++ 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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