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md200ns.log

Dmytro Kovalskyy, 11/15/2018 10:59 PM

 
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Log file opened on Thu Nov 15 15:57:31 2018
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Host: didesk  pid: 51574  rank ID: 0  number of ranks:  1
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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:   /usr/local/gromacs/bin/gmx
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Data prefix:  /usr/local/gromacs
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Working dir:  /home/dikov/Documents/DavidL/MD/GPU
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Command line:
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  gmx mdrun -deffnm md200ns -v
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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:        thread_mpi
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OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support:        CUDA
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SIMD instructions:  AVX_512
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FFT library:        fftw-3.3.7-sse2-avx
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      hwloc-1.11.6
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Tracing support:    disabled
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Built on:           2018-11-13 21:31:10
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Built by:           dikov@didesk [CMAKE]
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Build OS/arch:      Linux 4.15.0-36-generic x86_64
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Build CPU vendor:   Intel
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Build CPU brand:    Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz
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Build CPU family:   6   Model: 85   Stepping: 4
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Build CPU 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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C compiler:         /usr/bin/cc GNU 7.3.0
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C compiler flags:    -mavx512f -mfma     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /usr/bin/c++ GNU 7.3.0
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C++ compiler flags:  -mavx512f -mfma    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 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;-D_FORCE_INLINES;; ;-mavx512f;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
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CUDA driver:        10.0
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CUDA runtime:       10.0
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Running on 1 node with total 36 cores, 72 logical cores, 1 compatible GPU
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Hardware detected:
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  CPU info:
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    Vendor: Intel
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    Brand:  Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz
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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: 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  36] [   1  37] [   2  38] [   3  39] [   4  40] [   5  41] [   6  42] [   7  43] [   8  44] [   9  45] [  10  46] [  11  47] [  12  48] [  13  49] [  14  50] [  15  51] [  16  52] [  17  53]
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      Socket  1: [  18  54] [  19  55] [  20  56] [  21  57] [  22  58] [  23  59] [  24  60] [  25  61] [  26  62] [  27  63] [  28  64] [  29  65] [  30  66] [  31  67] [  32  68] [  33  69] [  34  70] [  35  71]
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    Numa nodes:
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      Node  0 (33376423936 bytes mem):   0  36   1  37   2  38   3  39   4  40   5  41   6  42   7  43   8  44   9  45  10  46  11  47  12  48  13  49  14  50  15  51  16  52  17  53
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      Node  1 (33792262144 bytes mem):  18  54  19  55  20  56  21  57  22  58  23  59  24  60  25  61  26  62  27  63  28  64  29  65  30  66  31  67  32  68  33  69  34  70  35  71
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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 2 ways
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      L2: 1048576 bytes, linesize 64 bytes, assoc. 16, shared 2 ways
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      L3: 25952256 bytes, linesize 64 bytes, assoc. 11, shared 36 ways
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    PCI devices:
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      0000:00:11.5  Id: 8086:a1d2  Class: 0x0106  Numa: 0
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      0000:00:16.2  Id: 8086:a1bc  Class: 0x0101  Numa: 0
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      0000:00:17.0  Id: 8086:2826  Class: 0x0104  Numa: 0
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      0000:02:00.0  Id: 8086:1533  Class: 0x0200  Numa: 0
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      0000:00:1f.6  Id: 8086:15b9  Class: 0x0200  Numa: 0
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      0000:91:00.0  Id: 144d:a808  Class: 0x0108  Numa: 0
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      0000:d5:00.0  Id: 10de:1bb0  Class: 0x0300  Numa: 0
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  GPU info:
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    Number of GPUs detected: 1
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    #0: NVIDIA Quadro P5000, compute cap.: 6.1, ECC:  no, stat: compatible
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
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Lindahl
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GROMACS: High performance molecular simulations through multi-level
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parallelism from laptops to supercomputers
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SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
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GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
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GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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Input Parameters:
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   integrator                     = md
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   tinit                          = 0
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   dt                             = 0.002
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   nsteps                         = 100000000
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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                        = 718849372
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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                         = 1000
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   nstcalcenergy                  = 100
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   nstenergy                      = 5000
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   nstxout-compressed             = 5000
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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                          = 0.931
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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                       = 0.9
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   epsilon-r                      = 1
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   epsilon-rf                     = inf
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   vdw-type                       = Cut-off
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   vdw-modifier                   = Potential-shift
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   rvdw-switch                    = 0
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   rvdw                           = 0.9
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   DispCorr                       = EnerPres
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   table-extension                = 1
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   fourierspacing                 = 0.16
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   fourier-nx                     = 52
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   fourier-ny                     = 60
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   fourier-nz                     = 72
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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                     = Isotropic
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   nstpcouple                     = 20
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   tau-p                          = 2
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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               = 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                   = 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:     16011.7      141396
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   ref-t:         300         300
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   tau-t:         0.1         0.1
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annealing:          No          No
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annealing-npoints:           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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Changing nstlist from 20 to 80, rlist from 0.931 to 1.049
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Using 1 MPI thread
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Using 36 OpenMP threads 
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1 GPU auto-selected for this run.
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Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
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  PP:0,PME:0
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Application clocks (GPU clocks) for Quadro P5000 are (4513,1733)
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Application clocks (GPU clocks) for Quadro P5000 are (4513,1733)
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Pinning threads with an auto-selected logical core stride of 2
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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 ++++
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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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Using a Gaussian width (1/beta) of 0.288146 nm for Ewald
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Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-05
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Initialized non-bonded Ewald correction tables, spacing: 8.85e-04 size: 1018
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Long Range LJ corr.: <C6> 3.3851e-04
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Generated table with 1024 data points for Ewald.
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Tabscale = 500 points/nm
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Generated table with 1024 data points for LJ6.
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Tabscale = 500 points/nm
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Generated table with 1024 data points for LJ12.
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Tabscale = 500 points/nm
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Generated table with 1024 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1024 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1024 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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Using a dual 8x4 pair-list setup updated with dynamic, rolling pruning:
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  outer list: updated every 80 steps, buffer 0.149 nm, rlist 1.049 nm
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  inner list: updated every 10 steps, buffer 0.003 nm, rlist 0.903 nm
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At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
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  outer list: updated every 80 steps, buffer 0.292 nm, rlist 1.192 nm
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  inner list: updated every 10 steps, buffer 0.043 nm, rlist 0.943 nm
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Using Lorentz-Berthelot Lennard-Jones combination rule
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Initializing LINear Constraint Solver
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377
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
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LINCS: A Linear Constraint Solver for molecular simulations
380
J. Comp. Chem. 18 (1997) pp. 1463-1472
381
-------- -------- --- Thank You --- -------- --------
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383
The number of constraints is 8054
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385
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
386
S. Miyamoto and P. A. Kollman
387
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
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Water Models
389
J. Comp. Chem. 13 (1992) pp. 952-962
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-------- -------- --- Thank You --- -------- --------
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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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398
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
399
G. Bussi, D. Donadio and M. Parrinello
400
Canonical sampling through velocity rescaling
401
J. Chem. Phys. 126 (2007) pp. 014101
402
-------- -------- --- Thank You --- -------- --------
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404
There are: 78646 Atoms
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Started mdrun on rank 0 Thu Nov 15 15:57:35 2018
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           Step           Time
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              0        0.00000
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-------------------------------------------------------
412
Program:     gmx mdrun, version 2018.3
413
Source file: src/gromacs/gpu_utils/cudautils.cu (line 110)
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415
Fatal error:
416
HtoD cudaMemcpyAsync failed: invalid argument
417

    
418
For more information and tips for troubleshooting, please check the GROMACS
419
website at http://www.gromacs.org/Documentation/Errors
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-------------------------------------------------------