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em.log

.log file obtained during energy minimization. - Siva Dasetty, 06/01/2018 05:36 PM

 
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Log file opened on Thu May 31 21:59:20 2018
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Host: node2002.palmetto.clemson.edu  pid: 19188  rank ID: 0  number of ranks:  1
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                       :-) GROMACS - gmx mdrun, 2018 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
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 Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  
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 Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
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    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
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  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff 
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   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk   
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   Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  
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   Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2017, 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
24
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
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Executable:   /home/sdasett/software/gromacs/version18/bin/gmx
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Data prefix:  /home/sdasett/software/gromacs/version18
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Working dir:  /scratch2/sdasett/test-cases/water-settles
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Command line:
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  gmx mdrun -s em.tpr -v -deffnm em -ntomp 6 -ntmpi 4
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GROMACS version:    2018
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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-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
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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:           2018-04-28 23:59:50
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Built by:           sdasett@node1279.palmetto.clemson.edu [CMAKE]
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Build OS/arch:      Linux 4.1.12-103.9.4.el7uek.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 v3 @ 2.50GHz
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Build CPU family:   6   Model: 63   Stepping: 2
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Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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C compiler:         /software/gcc/5.4.0/bin/gcc GNU 5.4.0
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C compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
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C++ compiler:       /software/gcc/5.4.0/bin/g++ GNU 5.4.0
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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:      /software/cuda-toolkit/8.0.44/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44
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CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-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_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;-Wno-deprecated-gpu-targets;;; ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
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CUDA driver:        9.0
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CUDA runtime:       8.0
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Running on 1 node with total 24 cores, 24 logical cores, 2 compatible GPUs
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Hardware detected:
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  CPU info:
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    Vendor: Intel
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    Brand:  Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
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    Family: 6   Model: 63   Stepping: 2
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    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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  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]
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      Socket  1: [  12] [  13] [  14] [  15] [  16] [  17] [  18] [  19] [  20] [  21] [  22] [  23]
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    Numa nodes:
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      Node  0 (66824003584 bytes mem):   0   1   2   3   4   5   6   7   8   9  10  11
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      Node  1 (67643322368 bytes mem):  12  13  14  15  16  17  18  19  20  21  22  23
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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: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways
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      L3: 31457280 bytes, linesize 64 bytes, assoc. 20, shared 12 ways
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    PCI devices:
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      0000:06:00.0  Id: 15b3:1007  Class: 0x0280  Numa: 0
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      0000:0b:00.0  Id: 10de:1023  Class: 0x0302  Numa: 0
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      0000:10:00.0  Id: 14e4:1665  Class: 0x0200  Numa: 0
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      0000:10:00.1  Id: 14e4:1665  Class: 0x0200  Numa: 0
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      0000:14:00.0  Id: 102b:0534  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: 14e4:168e  Class: 0x0200  Numa: 1
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      0000:81:00.1  Id: 14e4:168e  Class: 0x0200  Numa: 1
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      0000:86:00.0  Id: 10de:1023  Class: 0x0302  Numa: 1
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  GPU info:
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    Number of GPUs detected: 2
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    #0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC: yes, stat: compatible
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    #1: NVIDIA Tesla K40m, compute cap.: 3.5, ECC: yes, 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
114
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
130
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
132
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 --- -------- --------
142

    
143

    
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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                     = steep
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   tinit                          = 0
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   dt                             = 0.001
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   nsteps                         = 100000
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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                        = 62516664
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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                      = 1000
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   nstxout-compressed             = 0
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   compressed-x-precision         = 1000
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   cutoff-scheme                  = Verlet
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   nstlist                        = 10
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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                          = 1.05
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   coulombtype                    = PME
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   coulomb-modifier               = Potential-shift
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   rcoulomb-switch                = 0
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   rcoulomb                       = 1
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   epsilon-r                      = 1
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   epsilon-rf                     = inf
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   vdw-type                       = Cut-off
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   vdw-modifier                   = Potential-shift
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   rvdw-switch                    = 0
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   rvdw                           = 1
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.12
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   fourier-nx                     = 28
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   fourier-ny                     = 28
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   fourier-nz                     = 28
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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                         = No
225
   nsttcouple                     = -1
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = No
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   pcoupltype                     = Isotropic
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   nstpcouple                     = -1
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   tau-p                          = 1
232
   compressibility (3x3):
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      compressibility[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   ref-p (3x3):
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      ref-p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   refcoord-scaling               = No
241
   posres-com (3):
242
      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):
246
      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
256
   continuation                   = false
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 4
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   lincs-iter                     = 1
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   lincs-warnangle                = 30
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   nwall                          = 0
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   wall-type                      = 9-3
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   wall-r-linpot                  = -1
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   wall-atomtype[0]               = -1
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   wall-atomtype[1]               = -1
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   wall-density[0]                = 0
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   wall-density[1]                = 0
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   wall-ewald-zfac                = 3
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   pull                           = false
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   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:        5997
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   ref-t:           0
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   tau-t:           0
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annealing:          No
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annealing-npoints:           0
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   acc:	           0           0           0
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   nfreeze:           N           N           N
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   energygrp-flags[  0]: 0
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Initializing Domain Decomposition on 4 ranks
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NOTE: disabling dynamic load balancing as it is only supported with dynamics, not with integrator 'steep'.
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Dynamic load balancing: auto
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Initial maximum inter charge-group distances:
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    two-body bonded interactions: 0.152 nm, Exclusion, atoms 2534 2535
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Minimum cell size due to bonded interactions: 0.000 nm
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Using 0 separate PME ranks
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Optimizing the DD grid for 4 cells with a minimum initial size of 0.050 nm
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The maximum allowed number of cells is: X 64 Y 64 Z 64
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Domain decomposition grid 4 x 1 x 1, separate PME ranks 0
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PME domain decomposition: 4 x 1 x 1
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Domain decomposition rank 0, coordinates 0 0 0
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The initial number of communication pulses is: X 2
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The initial domain decomposition cell size is: X 0.80 nm
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.050 nm
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            two-body bonded interactions  (-rdd)   1.050 nm
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          multi-body bonded interactions  (-rdd)   0.800 nm
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              virtual site constructions  (-rcon)  0.800 nm
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  atoms separated by up to 5 constraints  (-rcon)  0.800 nm
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Using 4 MPI threads
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Using 6 OpenMP threads per tMPI thread
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On host node2002.palmetto.clemson.edu 2 GPUs auto-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:0,PP:1,PP:1
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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 K40m 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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Pinning threads with an auto-selected logical core stride of 1
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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 0.320163 nm for Ewald
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Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
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Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 1073
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Using GPU 8x8 nonbonded short-range kernels
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Using a 8x4 pair-list setup:
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  updated every 10 steps, buffer 0.050 nm, rlist 1.050 nm
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Using geometric Lennard-Jones combination rule
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Removing pbc first time
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Miyamoto and P. A. Kollman
389
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
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Water Models
391
J. Comp. Chem. 13 (1992) pp. 952-962
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-------- -------- --- Thank You --- -------- --------
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Linking all bonded interactions to atoms
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There are 1000 inter charge-group virtual sites,
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will an extra communication step for selected coordinates and forces
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Initiating Steepest Descents
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Atom distribution over 4 domains: av 1000 stddev 43 min 931 max 1044
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Started Steepest Descents on rank 0 Thu May 31 21:59:22 2018
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Steepest Descents:
404
   Tolerance (Fmax)   =  1.00000e+01
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   Number of steps    =       100000
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           Step           Time
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              0        0.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
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    3.42993e+04   -4.80696e+04    1.66194e+03   -1.21083e+04   -2.91242e+03
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DD  step 0 load imb.: force  0.4%
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           Step           Time
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              1        1.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
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    2.64691e+04   -4.83423e+04    1.65173e+03   -2.02215e+04   -4.75648e+03
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           Step           Time
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              2        2.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
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    1.90884e+04   -4.88205e+04    1.62008e+03   -2.81120e+04   -5.99026e+03
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           Step           Time
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              3        3.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
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    1.49182e+04   -4.94190e+04    1.55283e+03   -3.29479e+04   -6.50081e+03
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           Step           Time
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              4        4.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
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    1.24665e+04   -5.02834e+04    1.42686e+03   -3.63900e+04   -6.77428e+03
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           Step           Time
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              5        5.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
448
    1.11600e+04   -5.12584e+04    1.25313e+03   -3.88453e+04   -6.98918e+03
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           Step           Time
451
              6        6.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
455
    1.02038e+04   -5.24674e+04    1.04973e+03   -4.12138e+04   -7.23153e+03
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           Step           Time
458
              7        7.00000
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   Energies (kJ/mol)
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
462
    9.51823e+03   -5.33710e+04    8.78514e+02   -4.29743e+04   -7.39491e+03
463

    
464
           Step           Time
465
              8        8.00000
466

    
467
   Energies (kJ/mol)
468
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
469
    9.18059e+03   -5.38954e+04    8.25069e+02   -4.38897e+04   -7.50003e+03
470

    
471
           Step           Time
472
              9        9.00000
473

    
474
   Energies (kJ/mol)
475
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
476
    8.65443e+03   -5.51167e+04    6.50769e+02   -4.58115e+04   -7.66322e+03
477

    
478
           Step           Time
479
             10       10.00000
480

    
481
   Energies (kJ/mol)
482
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
483
    8.44828e+03   -5.54937e+04    6.37708e+02   -4.64077e+04   -7.72312e+03
484