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test_gmx51_1x16_cpu_bdver2.log

Szilárd Páll, 04/28/2015 03:06 AM

 
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Log file opened on Tue Apr 28 01:22:47 2015
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Host: tcbs22  pid: 15275  rank ID: 0  number of ranks:  1
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GROMACS:    gmx mdrun, VERSION 5.1-beta1-dev-20150427-07584c7
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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) 2001-2015, 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 5.1-beta1-dev-20150427-07584c7
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Executable:   /nethome/pszilard-projects/gromacs/gromacs-master/build_test/bin/gmx-noGPU
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Data prefix:  /nethome/pszilard-projects/gromacs/gromacs-master (source tree)
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Command line:
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  gmx-noGPU mdrun -quiet -v -resethway -noconfout -pin on -ntmpi 1 -ntomp 16 -nsteps 10000 -g test_gmx51_1x16_cpu_bdver2 -nb cpu
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Gromacs version:    VERSION 5.1-beta1-dev-20150427-07584c7
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GIT SHA1 hash:      07584c77d0534ec4e260a0147069f234b0e7d2d1
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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 = 32)
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GPU support:        disabled
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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:  enabled
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TNG support:        enabled
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Tracing support:    disabled
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Built on:           Tue Apr 28 00:14:52 CEST 2015
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Built by:           pszilard@tcbs22 [CMAKE]
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Build OS/arch:      Linux 3.13.0-46-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    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG -march=bdver2 -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   -std=c++0x  -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG -march=bdver2 -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds 
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Boost version:      1.55.0 (internal)
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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                           = 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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   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 
278
A smooth particle mesh Ewald method
279
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 Tue Apr 28 01:22:47 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    1.71087e+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    2.74515e+02    4.93064e-05
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step 5000: resetting all time and cycle counters
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Restarted time on rank 0 Tue Apr 28 01:23:20 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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    2.41445e+03    5.34852e+03    1.97405e+02    2.14064e+03    1.72503e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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    2.74463e+04   -2.77023e+05    2.52188e+03   -2.19703e+05    3.91008e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -1.80602e+05   -1.79403e+05    2.96767e+02    1.42923e+02    5.00786e-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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    2.49872e+03    5.31086e+03    1.82654e+02    2.08810e+03    1.69760e+04
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        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
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    2.73116e+04   -2.75860e+05    2.49442e+03   -2.18997e+05    3.94768e+04
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   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
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   -1.79521e+05   -1.79183e+05    2.99621e+02    6.30583e+01    0.00000e+00
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   Total Virial (kJ/mol)
390
    1.28092e+04   -2.61691e+01    8.74987e+01
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   -2.62872e+01    1.30085e+04   -1.20990e+02
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    8.74020e+01   -1.20958e+02    1.26988e+04
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   Pressure (bar)
395
    7.47071e+01    6.82566e+00   -1.86383e+01
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    6.84891e+00    2.08802e+01    2.51140e+01
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   -1.86193e+01    2.51076e+01    9.35877e+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
408
-----------------------------------------------------------------------------
409
 Pair Search distance check            2363.601994       21272.418     1.0
410
 NxN Ewald Elec. + LJ [F]             16060.814080     1060013.729    48.8
411
 NxN Ewald Elec. + LJ [V&F]             165.414240       17699.324     0.8
412
 NxN Ewald Elec. [F]                  12150.061072      741153.725    34.1
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 NxN Ewald Elec. [V&F]                  125.243632       10520.465     0.5
414
 1,4 nonbonded interactions              26.710341        2403.931     0.1
415
 Calc Weights                           254.270844        9153.750     0.4
416
 Spread Q Bspline                      5424.444672       10848.889     0.5
417
 Gather F Bspline                      5424.444672       32546.668     1.5
418
 3D-FFT                               30602.049186      244816.393    11.3
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 Solve PME                               15.683136        1003.721     0.0
420
 Shift-X                                  8.490948          50.946     0.0
421
 Angles                                  15.973194        2683.497     0.1
422
 Propers                                 25.545108        5849.830     0.3
423
 Impropers                                2.110422         438.968     0.0
424
 Virial                                   0.866643          15.600     0.0
425
 Stop-CM                                  0.864348           8.643     0.0
426
 Calc-Ekin                               16.964948         458.054     0.0
427
 Lincs                                    6.101220         366.073     0.0
428
 Lincs-Mat                              162.492492         649.970     0.0
429
 Constraint-V                            86.137224         689.098     0.0
430
 Constraint-Vir                           0.816204          19.589     0.0
431
 Settle                                  24.644928        7960.312     0.4
432
 Virtual Site 3                           0.666864          24.674     0.0
433
 Virtual Site 3fd                         0.944724          89.749     0.0
434
 Virtual Site 3fad                        0.383952          67.576     0.0
435
 Virtual Site 3out                        2.556312         222.399     0.0
436
 Virtual Site 4fdn                        0.742644         188.632     0.0
437
-----------------------------------------------------------------------------
438
 Total                                                 2171216.621   100.0
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-----------------------------------------------------------------------------
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     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
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444
On 1 MPI rank, each using 16 OpenMP threads
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446
 Computing:          Num   Num      Call    Wall time         Giga-Cycles
447
                     Ranks Threads  Count      (s)         total sum    %
448
-----------------------------------------------------------------------------
449
 Vsite constr.          1   16       5001       0.148          5.448   0.4
450
 Neighbor search        1   16        501       2.211         81.365   6.7
451
 Force                  1   16       5001      21.559        793.434  65.2
452
 PME mesh               1   16       5001       6.170        227.078  18.7
453
 NB X/F buffer ops.     1   16       9501       0.942         34.659   2.8
454
 Vsite spread           1   16       5052       0.167          6.152   0.5
455
 Update                 1   16       5001       0.270          9.930   0.8
456
 Constraints            1   16       5001       1.481         54.505   4.5
457
 Rest                                           0.116          4.269   0.4
458
-----------------------------------------------------------------------------
459
 Total                                         33.064       1216.840 100.0
460
-----------------------------------------------------------------------------
461
 Breakdown of PME mesh computation
462
-----------------------------------------------------------------------------
463
 PME spread/gather      1   16      10002       3.509        129.124  10.6
464
 PME 3D-FFT             1   16      10002       2.377         87.488   7.2
465
 PME solve Elec         1   16       5001       0.256          9.431   0.8
466
-----------------------------------------------------------------------------
467
 Breakdown of PP computation
468
-----------------------------------------------------------------------------
469
 NS grid local          1   16        501       0.129          4.738   0.4
470
 NS search local        1   16        501       2.000         73.597   6.0
471
 Bonded F               1   16       5001       0.711         26.168   2.2
472
 Listed buffer ops.     1   16       5001       2.862        105.333   8.7
473
 Nonbonded F            1   16       5001      17.714        651.927  53.6
474
 NB X buffer ops.       1   16       4500       0.220          8.095   0.7
475
 NB F buffer ops.       1   16       5001       0.721         26.529   2.2
476
-----------------------------------------------------------------------------
477

    
478
               Core t (s)   Wall t (s)        (%)
479
       Time:      527.518       33.064     1595.4
480
                 (ns/day)    (hour/ns)
481
Performance:       65.341        0.367
482
Finished mdrun on rank 0 Tue Apr 28 01:23:53 2015