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test_gmx50_1x16_cpu.log

Szilárd Páll, 04/28/2015 03:06 AM

 
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Log file opened on Mon Apr 27 16:33:41 2015
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Host: tcbs22  pid: 4812  rank ID: 0  number of ranks:  1
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GROMACS:    gmx mdrun, VERSION 5.0.5-dev-20141216-1433152
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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     Sebastian Fritsch  
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Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner    
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Per Larsson        Justin A. Lemkul   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     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) 2001-2014, 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 5.0.5-dev-20141216-1433152
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Executable:   /nethome/pszilard-projects/gromacs/gromacs-5.0/build_gcc48_pd/bin/gmx
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Library dir:  /nethome/pszilard/programs/gromacs-5.0-pd/share/gromacs/top
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Command line:
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  gmx mdrun -quiet -v -resethway -noconfout -pin on -ntmpi 1 -ntomp 16 -nsteps 10000 -g test_gmx50_1x16_cpu -nb cpu
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Gromacs version:    VERSION 5.0.5-dev-20141216-1433152
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GIT SHA1 hash:      1433152ec1b13e0698e22e54b572e8d1cd3627b2
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Branched from:      a0133801088e43fe074e0c78464357e95a01d223 (1 newer local commits)
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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
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GPU support:        enabled
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invsqrt routine:    gmx_software_invsqrt(x)
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SIMD instructions:  AVX_128_FMA
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FFT library:        fftw-3.3.2-sse2
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RDTSCP usage:       enabled
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C++11 compilation:  disabled
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TNG support:        enabled
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Tracing support:    disabled
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Built on:           Tue Jan 21 20:34:01 CET 2014
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Built by:           pszilard@tcbs22 [CMAKE]
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Build OS/arch:      Linux 3.5.0-45-generic x86_64
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Build CPU vendor:   AuthenticAMD
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Build CPU brand:    AMD Opteron(tm) Processor 6376
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Build CPU family:   21   Model: 2   Stepping: 0
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Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c fma fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop
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C compiler:         /usr/bin/gcc-4.8 GNU 4.8.1
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C compiler flags:    -mavx -mfma4 -mxop    -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG -march=bdver2 -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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C++ compiler:       /usr/bin/g++-4.8 GNU 4.8.1
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C++ compiler flags:  -mavx -mfma4 -mxop    -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG -march=bdver2 -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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Boost version:      1.55.0 (internal)
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CUDA compiler:      /opt/cuda-5.5.22/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2013 NVIDIA Corporation;Built on Wed_Jul_17_18:36:13_PDT_2013;Cuda compilation tools, release 5.5, V5.5.0
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CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35;-use_fast_math;-ccbin=/usr/bin/gcc-4.8;-Xcompiler;-fPIC ; ;-mavx;-mfma4;-mxop;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-march=bdver2;-fomit-frame-pointer;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
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CUDA driver:        7.0
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CUDA runtime:       5.50
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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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Changing rlist from 0.945 to 0.937 for non-bonded 4x4 atom kernels
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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                         = 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                        = 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                         = 0
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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                          = 0.937
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   rlistlong                      = 0.937
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   nstcalclr                      = 10
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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                       = No
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   table-extension                = 1
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   fourierspacing                 = 0.1125
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   fourier-nx                     = 56
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   fourier-ny                     = 56
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   fourier-nz                     = 56
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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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   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                     = 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                           = no
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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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   E-x:
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      n = 0
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   E-xt:
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      n = 0
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   E-y:
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      n = 0
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   E-yt:
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      n = 0
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   E-z:
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      n = 0
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   E-zt:
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      n = 0
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   swapcoords                     = no
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   adress                         = FALSE
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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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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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Overriding nsteps with value passed on the command line: 10000 steps, 50 ps
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Using 1 MPI thread
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Using 16 OpenMP threads 
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Detecting CPU SIMD instructions.
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Present hardware specification:
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Vendor: AuthenticAMD
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Brand:  AMD Opteron(tm) Processor 6376                 
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Family: 21  Model:  2  Stepping:  0
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Features: aes apic avx clfsh cmov cx8 cx16 f16c fma fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop
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SIMD instructions most likely to fit this hardware: AVX_128_FMA
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SIMD instructions selected at GROMACS compile time: AVX_128_FMA
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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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Will do ordinary reciprocal space Ewald sum.
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Using a Gaussian width (1/beta) of 0.288146 nm for Ewald
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Cut-off's:   NS: 0.937   Coulomb: 0.9   LJ: 0.9
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System total charge: 0.000
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Generated table with 968 data points for Ewald.
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Tabscale = 500 points/nm
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Generated table with 968 data points for LJ6.
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Tabscale = 500 points/nm
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Generated table with 968 data points for LJ12.
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Tabscale = 500 points/nm
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Generated table with 968 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 968 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 968 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Using AVX_128_FMA 4x4 non-bonded kernels
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Using Lorentz-Berthelot Lennard-Jones combination rule
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Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.000e-05
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Initialized non-bonded Ewald correction tables, spacing: 8.85e-04 size: 2190
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Removing pbc first time
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Pinning threads with an auto-selected logical core stride of 1
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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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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: 300.134 K
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Started mdrun on rank 0 Mon Apr 27 16:33:42 2015
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           Step           Time         Lambda
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              0        0.00000        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    1.71086e+02    2.16343e+03    1.68043e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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    2.70096e+04   -2.75073e+05    2.54483e+03   -2.18445e+05    3.94954e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -1.78949e+05   -1.78949e+05    2.99762e+02    2.74524e+02    4.92999e-05
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step 5000: resetting all time and cycle counters
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Restarted time on rank 0 Mon Apr 27 16:34:16 2015
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           Step           Time         Lambda
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          10000       50.00000        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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    2.37678e+03    5.28439e+03    1.66790e+02    2.12559e+03    1.70602e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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    2.73491e+04   -2.76632e+05    2.45197e+03   -2.19817e+05    3.93042e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -1.80513e+05   -1.79448e+05    2.98311e+02    3.27434e+02    4.55931e-05
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	<======  ###############  ==>
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	<====  A V E R A G E S  ====>
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	<==  ###############  ======>
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	Statistics over 10001 steps using 101 frames
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    2.51467e+03    5.31504e+03    1.82840e+02    2.08533e+03    1.68785e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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    2.73604e+04   -2.75904e+05    2.48869e+03   -2.19079e+05    3.95043e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -1.79575e+05   -1.79212e+05    2.99830e+02    6.15581e+01    0.00000e+00
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   Total Virial (kJ/mol)
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    1.28261e+04    7.00709e+01    1.25982e+00
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    7.00130e+01    1.28383e+04    6.29847e+01
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    1.11324e+00    6.29357e+01    1.29025e+04
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   Pressure (bar)
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    7.41954e+01   -1.28372e+01   -3.20026e+00
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   -1.28258e+01    6.18154e+01   -9.63721e+00
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   -3.17138e+00   -9.62757e+00    4.86635e+01
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	M E G A - F L O P S   A C C O U N T I N G
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 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
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 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
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 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
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 V&F=Potential and force  V=Potential only  F=Force only
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 Computing:                               M-Number         M-Flops  % Flops
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-----------------------------------------------------------------------------
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 Pair Search distance check            2361.995982       21257.964     1.0
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 NxN Ewald Elec. + LJ [F]             16040.171136     1058651.295    48.8
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 NxN Ewald Elec. + LJ [V&F]             165.230480       17679.661     0.8
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 NxN Ewald Elec. [F]                  12147.271792      740983.579    34.2
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 NxN Ewald Elec. [V&F]                  125.131824       10511.073     0.5
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 1,4 nonbonded interactions              26.710341        2403.931     0.1
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 Calc Weights                           254.270844        9153.750     0.4
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 Spread Q Bspline                      5424.444672       10848.889     0.5
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 Gather F Bspline                      5424.444672       32546.668     1.5
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 3D-FFT                               30602.049186      244816.393    11.3
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 Solve PME                               15.683136        1003.721     0.0
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 Shift-X                                  8.490948          50.946     0.0
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 Angles                                  15.973194        2683.497     0.1
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 Propers                                 25.545108        5849.830     0.3
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 Impropers                                2.110422         438.968     0.0
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 Virial                                   0.866643          15.600     0.0
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 Stop-CM                                  0.864348           8.643     0.0
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 Calc-Ekin                               16.964948         458.054     0.0
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 Lincs                                    6.101220         366.073     0.0
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 Lincs-Mat                              162.492492         649.970     0.0
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 Constraint-V                            86.137224         689.098     0.0
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 Constraint-Vir                           0.816204          19.589     0.0
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 Settle                                  24.644928        7960.312     0.4
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 Virtual Site 3                           0.666864          24.674     0.0
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 Virtual Site 3fd                         0.944724          89.749     0.0
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 Virtual Site 3fad                        0.383952          67.576     0.0
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 Virtual Site 3out                        2.556312         222.399     0.0
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 Virtual Site 4fdn                        0.742644         188.632     0.0
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-----------------------------------------------------------------------------
443
 Total                                                 2169640.532   100.0
444
-----------------------------------------------------------------------------
445

    
446

    
447
     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
448

    
449
On 1 MPI rank, each using 16 OpenMP threads
450

    
451
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
452
                     Ranks Threads  Count      (s)         total sum    %
453
-----------------------------------------------------------------------------
454
 Vsite constr.          1   16       5001       0.164          6.024   0.5
455
 Neighbor search        1   16        501       2.236         82.293   6.4
456
 Force                  1   16       5001      21.765        801.018  62.3
457
 PME mesh               1   16       5001       7.416        272.938  21.2
458
 NB X/F buffer ops.     1   16       9501       1.177         43.332   3.4
459
 Vsite spread           1   16       5052       0.174          6.416   0.5
460
 Update                 1   16       5001       0.163          5.981   0.5
461
 Constraints            1   16       5001       1.589         58.486   4.5
462
 Rest                                           0.272         10.028   0.8
463
-----------------------------------------------------------------------------
464
 Total                                         34.957       1286.516 100.0
465
-----------------------------------------------------------------------------
466
 Breakdown of PME mesh computation
467
-----------------------------------------------------------------------------
468
 PME spread/gather      1   16      10002       4.025        148.117  11.5
469
 PME 3D-FFT             1   16      10002       3.091        113.774   8.8
470
 PME solve Elec         1   16       5001       0.271          9.955   0.8
471
-----------------------------------------------------------------------------
472
 Breakdown of PP computation
473
-----------------------------------------------------------------------------
474
 NS grid local          1   16        501       0.136          4.994   0.4
475
 NS search local        1   16        501       2.004         73.760   5.7
476
 Bonded F               1   16       5001       3.455        127.152   9.9
477
 Nonbonded F            1   16       5001      18.031        663.596  51.6
478
 NB X buffer ops.       1   16       4500       0.229          8.420   0.7
479
 NB F buffer ops.       1   16       5001       0.947         34.864   2.7
480
-----------------------------------------------------------------------------
481

    
482
               Core t (s)   Wall t (s)        (%)
483
       Time:      557.771       34.957     1595.6
484
                 (ns/day)    (hour/ns)
485
Performance:       61.803        0.388
486
Finished mdrun on rank 0 Mon Apr 27 16:34:51 2015