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log running on gpu20, built on bs-gpu01 - Mark Abraham, 11/16/2018 01:27 AM

 
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Log file opened on Fri Nov 16 01:23:35 2018
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Host: gpu20  pid: 2644  rank ID: 0  number of ranks:  1
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            :-) GROMACS - gmx mdrun, 2018.3-dev-20180823-5d5eb38 (-:
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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-dev-20180823-5d5eb38
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Executable:   /nethome/mabraham/git/r2018/build-cmake-gcc-7.3-cuda-10.0-release/bin/gmx
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Data prefix:  /nethome/mabraham/git/r2018 (source tree)
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Working dir:  /nethome/mabraham/redmines/redmine-2762
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Command line:
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  gmx mdrun -deffnm quick -v
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GROMACS version:    2018.3-dev-20180823-5d5eb38
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GIT SHA1 hash:      5d5eb383a4b899b07faf1ab1635803225092ba8a
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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:  AVX2_256
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FFT library:        fftw-3.3.6-pl1-sse2
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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:           2018-11-15 23:19:11
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Built by:           mabraham@dev-gpu01 [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) Core(TM) i7-3930K CPU @ 3.20GHz
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Build CPU family:   6   Model: 45   Stepping: 7
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Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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C compiler:         /opt/tcbsys/gcc/7.3/bin/gcc GNU 7.3.0
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C compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /opt/tcbsys/gcc/7.3/bin/g++ GNU 7.3.0
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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:      /opt/tcbsys/cuda/10.0/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;; ;-march=core-avx2;-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 16 cores, 32 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) CPU E5-2620 v4 @ 2.10GHz
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    Family: 6   Model: 79   Stepping: 1
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    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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  Hardware topology: Full, with devices
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    Sockets, cores, and logical processors:
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      Socket  0: [   0  16] [   1  17] [   2  18] [   3  19] [   4  20] [   5  21] [   6  22] [   7  23]
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      Socket  1: [   8  24] [   9  25] [  10  26] [  11  27] [  12  28] [  13  29] [  14  30] [  15  31]
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    Numa nodes:
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      Node  0 (33635934208 bytes mem):   0  16   1  17   2  18   3  19   4  20   5  21   6  22   7  23
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      Node  1 (33797095424 bytes mem):   8  24   9  25  10  26  11  27  12  28  13  29  14  30  15  31
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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: 262144 bytes, linesize 64 bytes, assoc. 8, shared 2 ways
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      L3: 20971520 bytes, linesize 64 bytes, assoc. 20, shared 16 ways
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    PCI devices:
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      0000:02:00.0  Id: 10de:1b30  Class: 0x0300  Numa: 0
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      0000:00:11.4  Id: 8086:8d62  Class: 0x0106  Numa: 0
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      0000:04:00.0  Id: 8086:1528  Class: 0x0200  Numa: 0
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      0000:04:00.1  Id: 8086:1528  Class: 0x0200  Numa: 0
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      0000:06:00.0  Id: 1a03:2000  Class: 0x0300  Numa: 0
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      0000:00:1f.2  Id: 8086:8d02  Class: 0x0106  Numa: 0
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      0000:81:00.0  Id: 10de:1b30  Class: 0x0300  Numa: 1
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  GPU info:
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    Number of GPUs detected: 1
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    #0: NVIDIA Quadro P6000, 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
113
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                         = 10000
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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 16 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 P6000 are (4513,1657)
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Application clocks (GPU clocks) for Quadro P6000 are (4513,1657)
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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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++++ 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
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J. Comp. Chem. 18 (1997) pp. 1463-1472
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-------- -------- --- Thank You --- -------- --------
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The number of constraints is 8054
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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
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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++++ 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 Fri Nov 16 01:23:38 2018
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           Step           Time
408
              0        0.00000
409

    
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    1.67779e+04    2.36909e+04    9.57938e+02    8.54109e+03    1.06861e+05
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        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
414
    2.05014e+05   -1.54691e+04   -1.57409e+06    1.14580e+04   -1.21626e+06
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    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
416
    1.97480e+05   -1.01878e+06   -1.01873e+06    3.01781e+02   -3.31363e+02
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 Pressure (bar)   Constr. rmsd
418
   -1.65806e+02    3.01103e-05
419

    
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step  160: timed with pme grid 52 60 72, coulomb cutoff 0.900: 224.2 M-cycles
421
step  320: timed with pme grid 48 56 64, coulomb cutoff 0.944: 222.8 M-cycles
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step  480: timed with pme grid 44 52 60, coulomb cutoff 1.023: 245.6 M-cycles
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step  640: timed with pme grid 40 44 56, coulomb cutoff 1.155: 274.9 M-cycles
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step  800: timed with pme grid 40 48 56, coulomb cutoff 1.126: 265.3 M-cycles
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step  960: timed with pme grid 42 48 56, coulomb cutoff 1.078: 251.9 M-cycles
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           Step           Time
427
           1000        2.00000
428

    
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   Energies (kJ/mol)
430
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
431
    1.68927e+04    2.36071e+04    9.51294e+02    8.45874e+03    1.06528e+05
432
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
433
    2.04384e+05   -1.55164e+04   -1.56870e+06    6.18564e+03   -1.21721e+06
434
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
435
    1.96553e+05   -1.02066e+06   -1.01991e+06    3.00365e+02   -3.33388e+02
436
 Pressure (bar)   Constr. rmsd
437
   -1.47598e+02    2.75213e-05
438

    
439
step 1120: timed with pme grid 44 48 60, coulomb cutoff 1.059: 248.0 M-cycles
440
step 1280: timed with pme grid 44 52 60, coulomb cutoff 1.023: 244.1 M-cycles
441
step 1440: timed with pme grid 48 52 60, coulomb cutoff 1.007: 240.4 M-cycles
442
step 1600: timed with pme grid 48 52 64, coulomb cutoff 0.977: 232.9 M-cycles
443
step 1760: timed with pme grid 48 56 64, coulomb cutoff 0.944: 222.5 M-cycles
444
step 1920: timed with pme grid 52 56 72, coulomb cutoff 0.907: 225.0 M-cycles
445
           Step           Time
446
           2000        4.00000
447

    
448
   Energies (kJ/mol)
449
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
450
    1.65837e+04    2.35912e+04    9.59492e+02    8.53561e+03    1.06687e+05
451
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
452
    2.03744e+05   -1.54841e+04   -1.57268e+06    1.13212e+04   -1.21674e+06
453
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
454
    1.95762e+05   -1.02098e+06   -1.02013e+06    2.99156e+02   -3.32003e+02
455
 Pressure (bar)   Constr. rmsd
456
   -1.97237e+02    2.70771e-05
457

    
458
step 2080: timed with pme grid 52 60 72, coulomb cutoff 0.900: 222.4 M-cycles
459
              optimal pme grid 52 60 72, coulomb cutoff 0.900
460
           Step           Time
461
           3000        6.00000
462

    
463
   Energies (kJ/mol)
464
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
465
    1.66736e+04    2.36644e+04    9.52815e+02    8.48779e+03    1.06730e+05
466
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
467
    2.06814e+05   -1.54880e+04   -1.57587e+06    1.12006e+04   -1.21684e+06
468
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
469
    1.96504e+05   -1.02033e+06   -1.02026e+06    3.00289e+02   -3.32174e+02
470
 Pressure (bar)   Constr. rmsd
471
   -4.05136e+01    2.77024e-05
472

    
473
           Step           Time
474
           4000        8.00000
475

    
476
   Energies (kJ/mol)
477
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
478
    1.67373e+04    2.36817e+04    9.51193e+02    8.44166e+03    1.06782e+05
479
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
480
    2.09331e+05   -1.55430e+04   -1.58006e+06    1.12792e+04   -1.21840e+06
481
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
482
    1.97108e+05   -1.02129e+06   -1.02043e+06    3.01212e+02   -3.34532e+02
483
 Pressure (bar)   Constr. rmsd
484
    1.34941e+02    2.76706e-05
485

    
486
           Step           Time
487
           5000       10.00000
488

    
489
   Energies (kJ/mol)
490
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
491
    1.67019e+04    2.36966e+04    9.15413e+02    8.57482e+03    1.06715e+05
492
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
493
    2.07491e+05   -1.54497e+04   -1.57725e+06    1.14802e+04   -1.21712e+06
494
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
495
    1.96613e+05   -1.02051e+06   -1.02058e+06    3.00456e+02   -3.30532e+02
496
 Pressure (bar)   Constr. rmsd
497
    2.14296e+01    2.66959e-05
498

    
499
           Step           Time
500
           6000       12.00000
501

    
502
   Energies (kJ/mol)
503
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
504
    1.62464e+04    2.36031e+04    9.79088e+02    8.62207e+03    1.06495e+05
505
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
506
    2.05481e+05   -1.55281e+04   -1.57650e+06    1.13893e+04   -1.21921e+06
507
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
508
    1.96879e+05   -1.02233e+06   -1.02078e+06    3.00863e+02   -3.33889e+02
509
 Pressure (bar)   Constr. rmsd
510
   -1.29966e+01    2.60667e-05
511

    
512
           Step           Time
513
           7000       14.00000
514

    
515
   Energies (kJ/mol)
516
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
517
    1.65654e+04    2.36579e+04    9.97799e+02    8.56350e+03    1.06287e+05
518
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
519
    2.05204e+05   -1.54421e+04   -1.57455e+06    1.12191e+04   -1.21749e+06
520
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
521
    1.96199e+05   -1.02130e+06   -1.02091e+06    2.99823e+02   -3.30207e+02
522
 Pressure (bar)   Constr. rmsd
523
   -6.51409e+01    2.69637e-05
524

    
525
           Step           Time
526
           8000       16.00000
527

    
528
   Energies (kJ/mol)
529
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
530
    1.65405e+04    2.35556e+04    1.01641e+03    8.69755e+03    1.06477e+05
531
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
532
    2.07759e+05   -1.54815e+04   -1.57687e+06    1.11955e+04   -1.21711e+06
533
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
534
    1.96125e+05   -1.02099e+06   -1.02107e+06    2.99710e+02   -3.31893e+02
535
 Pressure (bar)   Constr. rmsd
536
    1.89731e+02    2.59564e-05
537

    
538
           Step           Time
539
           9000       18.00000
540

    
541
   Energies (kJ/mol)
542
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
543
    1.68634e+04    2.35546e+04    9.46829e+02    8.46186e+03    1.06524e+05
544
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
545
    2.04264e+05   -1.54322e+04   -1.57297e+06    1.13033e+04   -1.21648e+06
546
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
547
    1.96670e+05   -1.01981e+06   -1.02127e+06    3.00543e+02   -3.29787e+02
548
 Pressure (bar)   Constr. rmsd
549
   -2.35450e+02    2.73253e-05
550

    
551
           Step           Time
552
          10000       20.00000
553

    
554
Writing checkpoint, step 10000 at Fri Nov 16 01:23:57 2018
555

    
556

    
557
   Energies (kJ/mol)
558
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
559
    1.68681e+04    2.34801e+04    9.97799e+02    8.50723e+03    1.06489e+05
560
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
561
    2.08519e+05   -1.55317e+04   -1.57935e+06    1.12650e+04   -1.21875e+06
562
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
563
    1.96772e+05   -1.02198e+06   -1.02137e+06    3.00699e+02   -3.34048e+02
564
 Pressure (bar)   Constr. rmsd
565
    7.02886e+01    2.74140e-05
566

    
567
	<======  ###############  ==>
568
	<====  A V E R A G E S  ====>
569
	<==  ###############  ======>
570

    
571
	Statistics over 10001 steps using 101 frames
572

    
573
   Energies (kJ/mol)
574
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
575
    1.66433e+04    2.36255e+04    9.49281e+02    8.56159e+03    1.06644e+05
576
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
577
    2.06185e+05   -1.54966e+04   -1.57520e+06    1.05947e+04   -1.21749e+06
578
    Kinetic En.   Total Energy  Conserved En.    Temperature Pres. DC (bar)
579
    1.96277e+05   -1.02121e+06   -1.02058e+06    2.99944e+02   -3.32542e+02
580
 Pressure (bar)   Constr. rmsd
581
   -7.11588e+00    0.00000e+00
582

    
583
          Box-X          Box-Y          Box-Z
584
    8.00101e+00    9.02812e+00    1.07300e+01
585

    
586
   Total Virial (kJ/mol)
587
    6.53504e+04    1.14961e+02   -7.63021e+01
588
    1.16589e+02    6.54212e+04   -2.54370e+01
589
   -7.22639e+01   -1.98517e+01    6.60136e+04
590

    
591
   Pressure (bar)
592
   -6.19184e-01   -3.50136e+00    9.60262e+00
593
   -3.57126e+00   -2.11648e-01   -1.51216e-01
594
    9.42908e+00   -3.90915e-01   -2.05168e+01
595

    
596
      T-Protein  T-non-Protein
597
    2.99626e+02    2.99979e+02
598

    
599

    
600
	M E G A - F L O P S   A C C O U N T I N G
601

    
602
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
603
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
604
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
605
 V&F=Potential and force  V=Potential only  F=Force only
606

    
607
 Computing:                               M-Number         M-Flops  % Flops
608
-----------------------------------------------------------------------------
609
 Pair Search distance check             886.326048        7976.934     0.0
610
 NxN Ewald Elec. + LJ [F]            636295.200512    41995483.234    97.9
611
 NxN Ewald Elec. + LJ [V&F]            6486.610304      694067.303     1.6
612
 1,4 nonbonded interactions             212.331231       19109.811     0.0
613
 Shift-X                                  9.909396          59.456     0.0
614
 Angles                                 147.264725       24740.474     0.1
615
 Propers                                250.415039       57345.044     0.1
616
 Impropers                               13.661366        2841.564     0.0
617
 Virial                                  39.424191         709.635     0.0
618
 Stop-CM                                  7.943246          79.432     0.0
619
 Calc-Ekin                               78.803292        2127.689     0.0
620
 Lincs                                   80.548054        4832.883     0.0
621
 Lincs-Mat                             1767.176700        7068.707     0.0
622
 Constraint-V                           865.896581        6927.173     0.0
623
 Constraint-Vir                          39.342027         944.209     0.0
624
 Settle                                 234.933491       75883.518     0.2
625
-----------------------------------------------------------------------------
626
 Total                                                42900197.065   100.0
627
-----------------------------------------------------------------------------
628

    
629

    
630
     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
631

    
632
On 1 MPI rank, each using 16 OpenMP threads
633

    
634
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
635
                     Ranks Threads  Count      (s)         total sum    %
636
-----------------------------------------------------------------------------
637
 Neighbor search        1   16        126       0.546         18.363   2.9
638
 Launch GPU ops.        1   16      20002       1.423         47.832   7.5
639
 Force                  1   16      10001       1.410         47.392   7.4
640
 Wait PME GPU gather    1   16      10001       2.437         81.880  12.8
641
 Reduce GPU PME F       1   16      10001       0.366         12.290   1.9
642
 Wait GPU NB local      1   16      10001       3.626        121.847  19.0
643
 NB X/F buffer ops.     1   16      19876       1.406         47.241   7.4
644
 Write traj.            1   16          3       0.164          5.504   0.9
645
 Update                 1   16      10001       0.601         20.192   3.2
646
 Constraints            1   16      10001       1.413         47.497   7.4
647
 Rest                                           5.656        190.053  29.7
648
-----------------------------------------------------------------------------
649
 Total                                         19.049        640.090 100.0
650
-----------------------------------------------------------------------------
651

    
652
               Core t (s)   Wall t (s)        (%)
653
       Time:      304.781       19.049     1600.0
654
                 (ns/day)    (hour/ns)
655
Performance:       90.723        0.265
656
Finished mdrun on rank 0 Fri Nov 16 01:23:58 2018