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Log file opened on Wed Jul 23 15:10:37 2014
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Host: compute-0-1.local pid: 13596 rank ID: 0 number of ranks: 1
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GROMACS: gmx mdrun, VERSION 5.0 (double precision)
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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 (double precision)
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Executable: /home/leontyev/programs/bin/gromacs/gromacs-5.0/bin/gmx_d
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Library dir: /home/leontyev/programs/bin/gromacs/gromacs-5.0/share/gromacs/top
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Command line:
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mdrun_d -nt 1 -s Methylacetamide.tpr -o Methylacetamide.trr -x Methylacetamide.xtc -c Methylacetamide_fin.gro -g Methylacetamide.log
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Gromacs version: VERSION 5.0
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Precision: double
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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: disabled
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invsqrt routine: gmx_software_invsqrt(x)
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SIMD instructions: AVX_256
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FFT library: fftw-3.3.4-sse2-avx
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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: Fri Jul 18 22:55:04 PDT 2014
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Built by: leontyev@cluster01.interxinc.com [CMAKE]
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Build OS/arch: Linux 2.6.32-431.el6.x86_64 x86_64
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Build CPU vendor: GenuineIntel
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Build CPU brand: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
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Build CPU family: 6 Model: 45 Stepping: 7
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Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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C compiler: /export/apps/gcc/4.8.2/bin/gcc-gcc-4.8 GNU 4.8.2
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C compiler flags: -mavx -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -static-libgcc -static-libstdc++ -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG
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C++ compiler: /export/apps/gcc/4.8.2/bin/g++-gcc-4.8 GNU 4.8.2
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C++ compiler flags: -mavx -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG
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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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Input Parameters:
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integrator = md
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tinit = 0
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dt = 0.001
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nsteps = 10
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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 = 103
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bd-fric = 0
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ld-seed = 4079259596
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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 = 10000000
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nstvout = 10000000
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nstfout = 0
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nstlog = 1
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nstcalcenergy = 100
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nstenergy = 100
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nstxout-compressed = 0
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compressed-x-precision = 1000
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cutoff-scheme = Group
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nstlist = 5
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ns-type = Grid
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pbc = xyz
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periodic-molecules = FALSE
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verlet-buffer-tolerance = 0.005
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rlist = 1.3
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rlistlong = 1.3
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nstcalclr = 0
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coulombtype = PME
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coulomb-modifier = None
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rcoulomb-switch = 1.2
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rcoulomb = 1.3
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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 = None
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rvdw-switch = 0
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rvdw = 1.3
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DispCorr = EnerPres
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table-extension = 1
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fourierspacing = 0.12
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fourier-nx = 28
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fourier-ny = 28
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fourier-nz = 28
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pme-order = 4
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ewald-rtol = 1e-05
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ewald-rtol-lj = 0.001
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lj-pme-comb-rule = Geometric
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ewald-geometry = 0
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epsilon-surface = 0
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implicit-solvent = No
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gb-algorithm = Still
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nstgbradii = 1
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rgbradii = 1
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gb-epsilon-solvent = 80
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gb-saltconc = 0
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gb-obc-alpha = 1
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gb-obc-beta = 0.8
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gb-obc-gamma = 4.85
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gb-dielectric-offset = 0.009
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sa-algorithm = Ace-approximation
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sa-surface-tension = 2.05016
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tcoupl = Nose-Hoover
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nsttcouple = 5
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nh-chain-length = 1
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print-nose-hoover-chain-variables = FALSE
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pcoupl = Berendsen
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pcoupltype = Isotropic
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nstpcouple = 5
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tau-p = 5
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compressibility (3x3):
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compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
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compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
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compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
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ref-p (3x3):
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ref-p[ 0]={ 1.01325e+00, 0.00000e+00, 0.00000e+00}
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ref-p[ 1]={ 0.00000e+00, 1.01325e+00, 0.00000e+00}
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ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01325e+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 = 4
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lincs-iter = 1
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lincs-warnangle = 30
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nwall = 0
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wall-type = 9-3
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wall-r-linpot = -1
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wall-atomtype[0] = -1
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wall-atomtype[1] = -1
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wall-density[0] = 0
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wall-density[1] = 0
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wall-ewald-zfac = 3
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pull = 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: 7125
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ref-t: 298.15
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tau-t: 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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Using 1 MPI thread
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Detecting CPU SIMD instructions.
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Present hardware specification:
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Vendor: GenuineIntel
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Brand: Intel(R) Xeon(R) CPU E5-2665 0 @ 2.40GHz
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Family: 6 Model: 45 Stepping: 7
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Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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SIMD instructions most likely to fit this hardware: AVX_256
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SIMD instructions selected at GROMACS compile time: AVX_256
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NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
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removed in a future release when 'verlet' supports all interaction forms.
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Table routines are used for coulomb: FALSE
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Table routines are used for vdw: FALSE
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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 0.416211 nm for Ewald
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Cut-off's: NS: 1.3 Coulomb: 1.3 LJ: 1.3
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Long Range LJ corr.: <C6> 7.6923e-04
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System total charge: -0.000
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Generated table with 4600 data points for Ewald.
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Tabscale = 2000 points/nm
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Generated table with 4600 data points for LJ6.
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Tabscale = 2000 points/nm
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Generated table with 4600 data points for LJ12.
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Tabscale = 2000 points/nm
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Generated table with 4600 data points for 1-4 COUL.
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Tabscale = 2000 points/nm
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Generated table with 4600 data points for 1-4 LJ6.
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Tabscale = 2000 points/nm
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Generated table with 4600 data points for 1-4 LJ12.
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Tabscale = 2000 points/nm
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Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Ewald -0.000e+00
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Initialized non-bonded Ewald correction tables, spacing: 1.06e-03 size: 2164
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Removing pbc first time
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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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There are: 2376 Atoms
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Max number of connections per atom is 34
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Total number of connections is 35640
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Max number of graph edges per atom is 4
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Total number of graph edges is 4356
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Initial temperature: 294.781 K
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Started mdrun on rank 0 Wed Jul 23 15:10:37 2014
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Step Time Lambda
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0 0.00000 0.00000
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Grid: 3 x 3 x 3 cells
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Energies (kJ/mol)
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
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2.34312e+03 5.14151e+03 1.33092e+02 3.55685e+03 8.34370e+02
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Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
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-1.29147e+04 -3.28852e+03 -1.28735e+02 -1.32510e+03 -2.21748e+03
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Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
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-7.86555e+03 8.77660e+03 9.11051e+02 2.96302e+02 -1.32952e+02
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Pressure (bar)
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-1.06735e+03
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Step Time Lambda
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1 0.00100 0.00000
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Energies (kJ/mol)
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Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
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2.25870e+03 5.08286e+03 1.31952e+02 3.54895e+03 8.29584e+02
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|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
334
|
-1.29222e+04 -3.28496e+03 -1.28735e+02 -1.32305e+03 -2.21615e+03
|
|
335
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
336
|
-8.02299e+03 8.92015e+03 8.97160e+02 3.01148e+02 -1.32952e+02
|
|
337
|
Pressure (bar)
|
|
338
|
1.63500e+02
|
|
339
|
|
|
340
|
Step Time Lambda
|
|
341
|
2 0.00200 0.00000
|
|
342
|
|
|
343
|
Energies (kJ/mol)
|
|
344
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
345
|
2.18768e+03 4.97970e+03 1.29586e+02 3.53166e+03 8.23951e+02
|
|
346
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
347
|
-1.29347e+04 -3.28841e+03 -1.28741e+02 -1.31863e+03 -2.21457e+03
|
|
348
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
349
|
-8.23246e+03 9.11937e+03 8.86912e+02 3.07874e+02 -1.32965e+02
|
|
350
|
Pressure (bar)
|
|
351
|
2.07711e+03
|
|
352
|
|
|
353
|
Step Time Lambda
|
|
354
|
3 0.00300 0.00000
|
|
355
|
|
|
356
|
Energies (kJ/mol)
|
|
357
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
358
|
2.18880e+03 4.84707e+03 1.26382e+02 3.50555e+03 8.18121e+02
|
|
359
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
360
|
-1.29476e+04 -3.30159e+03 -1.28741e+02 -1.31679e+03 -2.21362e+03
|
|
361
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
362
|
-8.42244e+03 9.31325e+03 8.90811e+02 3.14420e+02 -1.32965e+02
|
|
363
|
Pressure (bar)
|
|
364
|
4.01299e+03
|
|
365
|
|
|
366
|
Step Time Lambda
|
|
367
|
4 0.00400 0.00000
|
|
368
|
|
|
369
|
Energies (kJ/mol)
|
|
370
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
371
|
2.20659e+03 4.70899e+03 1.22781e+02 3.47177e+03 8.13710e+02
|
|
372
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
373
|
-1.29569e+04 -3.32337e+03 -1.28741e+02 -1.32244e+03 -2.21411e+03
|
|
374
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
375
|
-8.62169e+03 9.51829e+03 8.96599e+02 3.21342e+02 -1.32965e+02
|
|
376
|
Pressure (bar)
|
|
377
|
5.47653e+03
|
|
378
|
|
|
379
|
Step Time Lambda
|
|
380
|
5 0.00500 0.00000
|
|
381
|
|
|
382
|
Energies (kJ/mol)
|
|
383
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
384
|
2.16582e+03 4.59404e+03 1.19137e+02 3.43206e+03 8.11586e+02
|
|
385
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
386
|
-1.29598e+04 -3.34981e+03 -1.28741e+02 -1.33819e+03 -2.21640e+03
|
|
387
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
388
|
-8.87029e+03 9.75911e+03 8.88816e+02 3.29472e+02 -1.32965e+02
|
|
389
|
Pressure (bar)
|
|
390
|
6.16503e+03
|
|
391
|
|
|
392
|
Step Time Lambda
|
|
393
|
6 0.00600 0.00000
|
|
394
|
|
|
395
|
Energies (kJ/mol)
|
|
396
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
397
|
2.09465e+03 4.52640e+03 1.15626e+02 3.38857e+03 8.11954e+02
|
|
398
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
399
|
-1.29565e+04 -3.37629e+03 -1.28741e+02 -1.36332e+03 -2.22027e+03
|
|
400
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
401
|
-9.10795e+03 9.98096e+03 8.73005e+02 3.36962e+02 -1.32965e+02
|
|
402
|
Pressure (bar)
|
|
403
|
6.05073e+03
|
|
404
|
|
|
405
|
Step Time Lambda
|
|
406
|
7 0.00700 0.00000
|
|
407
|
|
|
408
|
Energies (kJ/mol)
|
|
409
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
410
|
2.09536e+03 4.51630e+03 1.12242e+02 3.34337e+03 8.12749e+02
|
|
411
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
412
|
-1.29487e+04 -3.40256e+03 -1.28706e+02 -1.39359e+03 -2.22488e+03
|
|
413
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
414
|
-9.21845e+03 1.00881e+04 8.69608e+02 3.40578e+02 -1.32891e+02
|
|
415
|
Pressure (bar)
|
|
416
|
5.22124e+03
|
|
417
|
|
|
418
|
Step Time Lambda
|
|
419
|
8 0.00800 0.00000
|
|
420
|
|
|
421
|
Energies (kJ/mol)
|
|
422
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
423
|
2.18729e+03 4.55616e+03 1.08875e+02 3.29815e+03 8.16690e+02
|
|
424
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
425
|
-1.29436e+04 -3.42482e+03 -1.28706e+02 -1.42328e+03 -2.22920e+03
|
|
426
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
427
|
-9.18240e+03 1.00699e+04 8.87536e+02 3.39966e+02 -1.32891e+02
|
|
428
|
Pressure (bar)
|
|
429
|
4.56883e+03
|
|
430
|
|
|
431
|
Step Time Lambda
|
|
432
|
9 0.00900 0.00000
|
|
433
|
|
|
434
|
Energies (kJ/mol)
|
|
435
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
436
|
2.26212e+03 4.62521e+03 1.05429e+02 3.25408e+03 8.21330e+02
|
|
437
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
438
|
-1.29445e+04 -3.44812e+03 -1.28706e+02 -1.44546e+03 -2.23212e+03
|
|
439
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
440
|
-9.13067e+03 1.00356e+04 9.04910e+02 3.38806e+02 -1.32891e+02
|
|
441
|
Pressure (bar)
|
|
442
|
4.49459e+03
|
|
443
|
|
|
444
|
Step Time Lambda
|
|
445
|
10 0.01000 0.00000
|
|
446
|
|
|
447
|
Writing checkpoint, step 10 at Wed Jul 23 15:10:37 2014
|
|
448
|
|
|
449
|
|
|
450
|
Energies (kJ/mol)
|
|
451
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
452
|
2.21648e+03 4.69922e+03 1.01927e+02 3.21190e+03 8.26075e+02
|
|
453
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
454
|
-1.29541e+04 -3.47543e+03 -1.28706e+02 -1.45550e+03 -2.23304e+03
|
|
455
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
456
|
-9.19120e+03 1.00913e+04 9.00066e+02 3.40686e+02 -1.32891e+02
|
|
457
|
Pressure (bar)
|
|
458
|
5.34039e+03
|
|
459
|
|
|
460
|
<====== ############### ==>
|
|
461
|
<==== A V E R A G E S ====>
|
|
462
|
<== ############### ======>
|
|
463
|
|
|
464
|
Statistics over 11 steps using 11 frames
|
|
465
|
|
|
466
|
Energies (kJ/mol)
|
|
467
|
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
|
|
468
|
2.20060e+03 4.75250e+03 1.18821e+02 3.41299e+03 8.20011e+02
|
|
469
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
|
470
|
-1.29439e+04 -3.36035e+03 -1.28727e+02 -1.36594e+03 -2.22108e+03
|
|
471
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
|
472
|
-8.71510e+03 9.60660e+03 8.91498e+02 3.24323e+02 -1.32936e+02
|
|
473
|
Pressure (bar)
|
|
474
|
3.86396e+03
|
|
475
|
|
|
476
|
Box-X Box-Y Box-Z
|
|
477
|
3.18007e+00 3.18007e+00 3.18007e+00
|
|
478
|
|
|
479
|
Total Virial (kJ/mol)
|
|
480
|
-6.14293e+02 -2.49406e+02 -2.10495e+02
|
|
481
|
-2.49406e+02 -7.39892e+02 -5.44235e+02
|
|
482
|
-2.10495e+02 -5.44235e+02 -2.64323e+02
|
|
483
|
|
|
484
|
Pressure (bar)
|
|
485
|
4.06644e+03 3.07847e+02 3.03916e+02
|
|
486
|
3.07847e+02 3.96556e+03 4.76728e+02
|
|
487
|
3.03916e+02 4.76728e+02 3.55988e+03
|
|
488
|
|
|
489
|
|
|
490
|
M E G A - F L O P S A C C O U N T I N G
|
|
491
|
|
|
492
|
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
|
|
493
|
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
|
|
494
|
W3=SPC/TIP3p W4=TIP4p (single or pairs)
|
|
495
|
V&F=Potential and force V=Potential only F=Force only
|
|
496
|
|
|
497
|
Computing: M-Number M-Flops % Flops
|
|
498
|
-----------------------------------------------------------------------------
|
|
499
|
NB Elec. [V&F] 66.822288 66.822 11.6
|
|
500
|
NB VdW & Elec. [V&F] 416.214936 416.215 72.4
|
|
501
|
1,4 nonbonded interactions 0.034848 3.136 0.5
|
|
502
|
Calc Weights 0.078408 2.823 0.5
|
|
503
|
Spread Q Bspline 1.672704 3.345 0.6
|
|
504
|
Gather F Bspline 1.672704 10.036 1.7
|
|
505
|
3D-FFT 6.965046 55.720 9.7
|
|
506
|
Solve PME 0.008624 0.552 0.1
|
|
507
|
NS-Pairs 0.066219 1.391 0.2
|
|
508
|
Reset In Box 0.000594 0.002 0.0
|
|
509
|
Shift-X 0.052272 0.314 0.1
|
|
510
|
CG-CoM 0.007128 0.021 0.0
|
|
511
|
Bonds 0.023958 1.414 0.2
|
|
512
|
Angles 0.039204 6.586 1.1
|
|
513
|
Propers 0.004356 0.998 0.2
|
|
514
|
RB-Dihedrals 0.015246 3.766 0.7
|
|
515
|
Virial 0.026631 0.479 0.1
|
|
516
|
Stop-CM 0.004752 0.048 0.0
|
|
517
|
P-Coupling 0.026136 0.157 0.0
|
|
518
|
Calc-Ekin 0.028512 0.770 0.1
|
|
519
|
-----------------------------------------------------------------------------
|
|
520
|
Total 574.594 100.0
|
|
521
|
-----------------------------------------------------------------------------
|
|
522
|
|
|
523
|
|
|
524
|
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
|
|
525
|
|
|
526
|
On 1 MPI rank
|
|
527
|
|
|
528
|
Computing: Num Num Call Wall time Giga-Cycles
|
|
529
|
Ranks Threads Count (s) total sum %
|
|
530
|
-----------------------------------------------------------------------------
|
|
531
|
Neighbor search 1 1 3 0.018 0.043 8.2
|
|
532
|
Force 1 1 11 0.167 0.402 76.4
|
|
533
|
PME mesh 1 1 11 0.012 0.029 5.5
|
|
534
|
Write traj. 1 1 2 0.020 0.047 9.0
|
|
535
|
Update 1 1 11 0.001 0.002 0.3
|
|
536
|
Rest 0.001 0.003 0.6
|
|
537
|
-----------------------------------------------------------------------------
|
|
538
|
Total 0.219 0.526 100.0
|
|
539
|
-----------------------------------------------------------------------------
|
|
540
|
Breakdown of PME mesh computation
|
|
541
|
-----------------------------------------------------------------------------
|
|
542
|
PME spread/gather 1 1 22 0.005 0.012 2.3
|
|
543
|
PME 3D-FFT 1 1 22 0.004 0.009 1.7
|
|
544
|
PME solve Elec 1 1 11 0.003 0.008 1.4
|
|
545
|
-----------------------------------------------------------------------------
|
|
546
|
|
|
547
|
Core t (s) Wall t (s) (%)
|
|
548
|
Time: 0.207 0.219 94.8
|
|
549
|
(ns/day) (hour/ns)
|
|
550
|
Performance: 4.344 5.525
|
|
551
|
Finished mdrun on rank 0 Wed Jul 23 15:10:37 2014
|