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test-gmx19_gcc7_1x16.log

Szilárd Páll, 12/12/2018 07:48 PM

 
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           :-) GROMACS - gmx mdrun, 2019-rc1-dev-20181211-da04714 (-:
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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      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
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 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
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  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
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  Aleksei Iupinov   Christoph Junghans     Joe Jordan     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     Erik Marklund   
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    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
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    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
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   Alfons Sijbers     Peter Tieleman      Jon Vincent      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) 2001-2018, 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 2019-rc1-dev-20181211-da04714
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Executable:   /nethome/pszilard-projects/gromacs/gromacs-19/build_AVX2_256_gcc7_cuda9.2/bin/gmx
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Data prefix:  /nethome/pszilard-projects/gromacs/gromacs-19 (source tree)
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Working dir:  /nethome/pszilard-projects/gromacs/testing/rnase_cut0.8/rnase_dodec_vsite/gmx-ver-cmp/gmx18-19
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Process ID:   17662
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Command line:
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  gmx mdrun -v -resethway -noconfout -pin on -nb gpu -pme cpu -ntmpi 1 -ntomp 16 -nsteps 20000 -g test-gmx19_gcc7_1x16
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GROMACS version:    2019-rc1-dev-20181211-da04714
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GIT SHA1 hash:      da0471447a8c8ee99d4034c13dc7e59cfd0d5607
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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-3.3.7-sse2-avx-avx2-avx2_128
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RDTSCP usage:       enabled
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TNG support:        enabled
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Hwloc support:      disabled
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Tracing support:    disabled
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C compiler:         /opt/tcbsys/gcc/7.3/bin/gcc-7 GNU 7.3.0
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C compiler flags:    -mavx2 -mfma    -Werror=format-overflow -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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C++ compiler:       /opt/tcbsys/gcc/7.3/bin/g++-7 GNU 7.3.0
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C++ compiler flags:  -mavx2 -mfma    -std=c++11  -Wformat-overflow -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations -Wall  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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CUDA compiler:      /opt/tcbsys/cuda/9.2/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on Tue_Jun_12_23:07:04_CDT_2018;Cuda compilation tools, release 9.2, V9.2.148
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CUDA compiler flags:-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_70,code=sm_70;-use_fast_math;-D_FORCE_INLINES;; ;-mavx2;-mfma;-std=c++11;-Wformat-overflow;-Wundef;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wmissing-declarations;-Wall;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
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CUDA driver:        10.0
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CUDA runtime:       9.20
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Running on 1 node with total 8 cores, 16 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) Core(TM) i7-5960X CPU @ 3.00GHz
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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: Basic
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    Sockets, cores, and logical processors:
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      Socket  0: [   0   8] [   1   9] [   2  10] [   3  11] [   4  12] [   5  13] [   6  14] [   7  15]
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  GPU info:
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    Number of GPUs detected: 1
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    #0: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, 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                             = 0.005
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   nsteps                         = -1
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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                        = 1993
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   emtol                          = 10
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   emstep                         = 0.01
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   niter                          = 20
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   fcstep                         = 0
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   nstcgsteep                     = 1000
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   nbfgscorr                      = 10
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   rtpi                           = 0.05
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   nstxout                        = 0
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   nstvout                        = 0
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   nstfout                        = 0
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   nstlog                         = 5000
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   nstcalcenergy                  = 100
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   nstenergy                      = 500
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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                          = 0.851
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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                       = 0.8
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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                           = 0.8
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   DispCorr                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.1
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   fourier-nx                     = 64
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   fourier-ny                     = 64
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   fourier-nz                     = 64
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   pme-order                      = 4
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   ewald-rtol                     = 1e-05
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   ewald-rtol-lj                  = 1e-05
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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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   tcoupl                         = V-rescale
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   nsttcouple                     = 10
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   nh-chain-length                = 0
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   print-nose-hoover-chain-variables = false
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   pcoupl                         = No
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   pcoupltype                     = Isotropic
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   nstpcouple                     = -1
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   tau-p                          = 1
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   compressibility (3x3):
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      compressibility[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   ref-p (3x3):
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      ref-p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   refcoord-scaling               = No
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   posres-com (3):
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      posres-com[0]= 0.00000e+00
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      posres-com[1]= 0.00000e+00
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      posres-com[2]= 0.00000e+00
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   posres-comB (3):
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      posres-comB[0]= 0.00000e+00
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      posres-comB[1]= 0.00000e+00
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      posres-comB[2]= 0.00000e+00
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   QMMM                           = false
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   QMconstraints                  = 0
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   QMMMscheme                     = 0
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   MMChargeScaleFactor            = 1
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qm-opts:
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   ngQM                           = 0
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   constraint-algorithm           = Lincs
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   continuation                   = false
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   Shake-SOR                      = false
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   shake-tol                      = 0.0001
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   lincs-order                    = 6
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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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grpopts:
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   nrdf:       31693
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   ref-t:         300
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   tau-t:         0.1
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annealing:          No
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annealing-npoints:           0
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   acc:	           0           0           0
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   nfreeze:           N           N           N
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   energygrp-flags[  0]: 0
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The -nsteps functionality is deprecated, and may be removed in a future version. Consider using gmx convert-tpr -nsteps or changing the appropriate .mdp file field.
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Overriding nsteps with value passed on the command line: 20000 steps, 100 ps
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Changing rlist from 0.851 to 0.842 for non-bonded 8x4 atom kernels
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Changing nstlist from 10 to 40, rlist from 0.842 to 0.968
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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 1 GPU task in the 1 rank on this node:
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  PP:0
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PP tasks will do (non-perturbed) short-ranged and most bonded interactions on the GPU
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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 0.25613 nm for Ewald
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Potential shift: LJ r^-12: -1.455e+01 r^-6: -3.815e+00, Ewald -1.250e-05
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Initialized non-bonded Ewald correction tables, spacing: 8.35e-04 size: 960
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Generated table with 983 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 983 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 983 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 40 steps, buffer 0.168 nm, rlist 0.968 nm
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  inner list: updated every  4 steps, buffer 0.003 nm, rlist 0.803 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 40 steps, buffer 0.314 nm, rlist 1.114 nm
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  inner list: updated every  4 steps, buffer 0.041 nm, rlist 0.841 nm
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Using Lorentz-Berthelot Lennard-Jones combination rule
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Removing pbc first time
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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
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P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 116-122
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-------- -------- --- Thank You --- -------- --------
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The number of constraints is 1220
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249 constraints are involved in constraint triangles,
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will apply an additional matrix expansion of order 6 for couplings
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between constraints inside triangles
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Miyamoto and P. A. Kollman
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SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
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Water Models
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J. Comp. Chem. 13 (1992) pp. 952-962
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-------- -------- --- Thank You --- -------- --------
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The -noconfout functionality is deprecated, and may be removed in a future version.
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Intra-simulation communication will occur every 10 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 ++++
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G. Bussi, D. Donadio and M. Parrinello
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Canonical sampling through velocity rescaling
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J. Chem. Phys. 126 (2007) pp. 014101
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-------- -------- --- Thank You --- -------- --------
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There are: 15900 Atoms
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There are: 1048 VSites
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Constraining the starting coordinates (step 0)
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Constraining the coordinates at t0-dt (step 0)
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RMS relative constraint deviation after constraining: 2.85e-05
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Initial temperature: 300.135 K
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Started mdrun on rank 0 Wed Dec 12 18:50:23 2018
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The -resethway functionality is deprecated, and may be removed in a future version.
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           Step           Time
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              0        0.00000
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    2.61927e+03    5.31560e+03    1.71085e+02    2.16343e+03    1.68043e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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    2.83951e+04   -2.76663e+05    4.12171e+03   -2.17073e+05    3.94952e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -1.77578e+05   -1.77578e+05    2.99762e+02    4.15816e+02    4.93328e-05
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step   80: timed with pme grid 64 64 64, coulomb cutoff 0.800: 93.1 M-cycles
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step  160: timed with pme grid 56 56 56, coulomb cutoff 0.886: 76.4 M-cycles
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step  240: timed with pme grid 48 48 48, coulomb cutoff 1.033: 68.3 M-cycles
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step  320: timed with pme grid 44 44 44, coulomb cutoff 1.127: 76.5 M-cycles
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step  400: timed with pme grid 40 40 40, coulomb cutoff 1.240: 83.6 M-cycles
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step  480: timed with pme grid 42 42 42, coulomb cutoff 1.181: 78.4 M-cycles
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step  560: timed with pme grid 44 44 44, coulomb cutoff 1.127: 73.5 M-cycles
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step  640: timed with pme grid 48 48 48, coulomb cutoff 1.033: 68.6 M-cycles
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step  720: timed with pme grid 52 52 52, coulomb cutoff 0.954: 76.3 M-cycles
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step  800: timed with pme grid 56 56 56, coulomb cutoff 0.886: 76.5 M-cycles
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step  880: timed with pme grid 60 60 60, coulomb cutoff 0.827: 84.2 M-cycles
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step  960: timed with pme grid 44 44 44, coulomb cutoff 1.127: 74.0 M-cycles
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step 1040: timed with pme grid 48 48 48, coulomb cutoff 1.033: 68.7 M-cycles
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step 1120: timed with pme grid 52 52 52, coulomb cutoff 0.954: 76.6 M-cycles
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step 1200: timed with pme grid 56 56 56, coulomb cutoff 0.886: 76.7 M-cycles
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              optimal pme grid 48 48 48, coulomb cutoff 1.033
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           Step           Time
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           5000       25.00000
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    2.47838e+03    5.30416e+03    2.00450e+02    2.05557e+03    1.69325e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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    2.82522e+04   -2.74106e+05    1.46892e+03   -2.17414e+05    3.90316e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -1.78382e+05   -1.77854e+05    2.96244e+02    1.83988e+01    5.43316e-05
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step 10000: resetting all time and cycle counters
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Restarted time on rank 0 Wed Dec 12 18:50:33 2018
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           Step           Time
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          10000       50.00000
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    2.59035e+03    5.27221e+03    1.76942e+02    2.04568e+03    1.69511e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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    2.93054e+04   -2.76299e+05    1.50222e+03   -2.18455e+05    3.94966e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -1.78959e+05   -1.78101e+05    2.99773e+02    2.04776e+02    5.53964e-05
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           Step           Time
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          15000       75.00000
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    2.46153e+03    5.27687e+03    1.76129e+02    2.06692e+03    1.68901e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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    2.87997e+04   -2.74915e+05    1.47215e+03   -2.17772e+05    3.95004e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
431
   -1.78272e+05   -1.78401e+05    2.99802e+02   -4.57840e-02    5.37144e-05
432

    
433
           Step           Time
434
          20000      100.00000
435

    
436
   Energies (kJ/mol)
437
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
438
    2.38814e+03    5.29337e+03    1.91382e+02    2.12067e+03    1.68574e+04
439
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
440
    2.89112e+04   -2.74680e+05    1.48508e+03   -2.17432e+05    3.93965e+04
441
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
442
   -1.78036e+05   -1.78637e+05    2.99013e+02    3.04130e+02    5.13721e-05
443

    
444
	<======  ###############  ==>
445
	<====  A V E R A G E S  ====>
446
	<==  ###############  ======>
447

    
448
	Statistics over 20001 steps using 201 frames
449

    
450
   Energies (kJ/mol)
451
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
452
    2.47419e+03    5.30715e+03    1.84506e+02    2.08297e+03    1.69161e+04
453
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
454
    2.87652e+04   -2.75000e+05    1.51910e+03   -2.17751e+05    3.95417e+04
455
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
456
   -1.78209e+05   -1.78113e+05    3.00115e+02    2.02215e+02    0.00000e+00
457

    
458
   Total Virial (kJ/mol)
459
    1.22607e+04   -1.12747e+02    5.16805e+01
460
   -1.12720e+02    1.20543e+04    3.58043e+01
461
    5.16243e+01    3.57284e+01    1.21472e+04
462

    
463
   Pressure (bar)
464
    1.88058e+02    2.34141e+01   -1.26818e+01
465
    2.34088e+01    2.16885e+02   -9.81290e+00
466
   -1.26707e+01   -9.79796e+00    2.01703e+02
467

    
468

    
469
       P P   -   P M E   L O A D   B A L A N C I N G
470

    
471
 PP/PME load balancing changed the cut-off and PME settings:
472
           particle-particle                    PME
473
            rcoulomb  rlist            grid      spacing   1/beta
474
   initial  0.800 nm  0.803 nm      64  64  64   0.097 nm  0.256 nm
475
   final    1.033 nm  1.036 nm      48  48  48   0.129 nm  0.331 nm
476
 cost-ratio           2.15             0.42
477
 (note that these numbers concern only part of the total PP and PME load)
478

    
479

    
480
	M E G A - F L O P S   A C C O U N T I N G
481

    
482
 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
483
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
484
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
485
 V&F=Potential and force  V=Potential only  F=Force only
486

    
487
 Computing:                               M-Number         M-Flops  % Flops
488
-----------------------------------------------------------------------------
489
 Pair Search distance check             435.400880        3918.608     0.0
490
 NxN Ewald Elec. + LJ [F]            175594.312384    11589224.617    94.9
491
 NxN Ewald Elec. + LJ [V&F]            1791.397568      191679.540     1.6
492
 Calc Weights                           508.490844       18305.670     0.1
493
 Spread Q Bspline                     10847.804672       21695.609     0.2
494
 Gather F Bspline                     10847.804672       65086.828     0.5
495
 3D-FFT                               37062.825912      296502.607     2.4
496
 Solve PME                               23.042304        1474.707     0.0
497
 Shift-X                                  4.253948          25.524     0.0
498
 Virial                                   1.716293          30.893     0.0
499
 Stop-CM                                  1.711748          17.117     0.0
500
 Calc-Ekin                               33.912948         915.650     0.0
501
 Lincs                                   12.201220         732.073     0.0
502
 Lincs-Mat                              324.952492        1299.810     0.0
503
 Constraint-V                           172.257224        1378.058     0.0
504
 Constraint-Vir                           1.616404          38.794     0.0
505
 Settle                                  49.284928       15919.032     0.1
506
 Virtual Site 3                           1.333464          49.338     0.0
507
 Virtual Site 3fd                         1.889074         179.462     0.0
508
 Virtual Site 3fad                        0.767752         135.124     0.0
509
 Virtual Site 3out                        5.111612         444.710     0.0
510
 Virtual Site 4fdn                        1.484994         377.188     0.0
511
-----------------------------------------------------------------------------
512
 Total                                                12209430.961   100.0
513
-----------------------------------------------------------------------------
514

    
515

    
516
     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
517

    
518
On 1 MPI rank, each using 16 OpenMP threads
519

    
520
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
521
                     Ranks Threads  Count      (s)         total sum    %
522
-----------------------------------------------------------------------------
523
 Vsite constr.          1   16      10001       0.097          4.642   1.7
524
 Neighbor search        1   16        251       0.230         11.023   4.0
525
 Launch GPU ops.        1   16      10001       0.494         23.719   8.6
526
 Force                  1   16      10001       0.064          3.049   1.1
527
 PME mesh               1   16      10001       3.592        172.427  62.5
528
 Wait Bonded GPU        1   16        101       0.002          0.114   0.0
529
 Wait GPU NB local      1   16      10001       0.167          8.011   2.9
530
 NB X/F buffer ops.     1   16      19751       0.168          8.073   2.9
531
 Vsite spread           1   16      10102       0.119          5.707   2.1
532
 Update                 1   16      10001       0.151          7.242   2.6
533
 Constraints            1   16      10001       0.574         27.539  10.0
534
 Rest                                           0.093          4.446   1.6
535
-----------------------------------------------------------------------------
536
 Total                                          5.750        275.994 100.0
537
-----------------------------------------------------------------------------
538
 Breakdown of PME mesh computation
539
-----------------------------------------------------------------------------
540
 PME spread             1   16      10001       1.213         58.200  21.1
541
 PME gather             1   16      10001       0.842         40.403  14.6
542
 PME 3D-FFT             1   16      20002       1.347         64.647  23.4
543
 PME solve Elec         1   16      10001       0.165          7.944   2.9
544
-----------------------------------------------------------------------------
545
 Breakdown of PP computation
546
-----------------------------------------------------------------------------
547
 NS grid local          1   16        251       0.042          2.006   0.7
548
 NS search local        1   16        251       0.168          8.074   2.9
549
 Launch NB GPU tasks    1   16      20002       0.277         13.298   4.8
550
 Launch Bonded GPU t    1   16      10001       0.191          9.168   3.3
551
 NB X buffer ops.       1   16       9750       0.083          3.984   1.4
552
 NB F buffer ops.       1   16      10001       0.084          4.039   1.5
553
-----------------------------------------------------------------------------
554

    
555
               Core t (s)   Wall t (s)        (%)
556
       Time:       91.891        5.750     1598.1
557
                 (ns/day)    (hour/ns)
558
Performance:      751.394        0.032
559
Finished mdrun on rank 0 Wed Dec 12 18:50:39 2018
560