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grompp_sim.txt

Daniel Kozuch, 11/19/2017 11:06 PM

 
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                      :-) GROMACS - gmx grompp, 2016.3 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
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 Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  
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 Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
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    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
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  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff    Erik Marklund   
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   Teemu Murtola       Szilard Pall       Sander Pronk      Roland Schulz   
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  Alexey Shvetsov     Michael Shirts     Alfons Sijbers     Peter Tieleman  
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  Teemu Virolainen  Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2017, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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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 grompp, version 2016.3
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[REDACTED]
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Command line:
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  gmx_163_gpu grompp -f sim.mdp -c 1tsk_eq.gro -p topol.top -t 1tsk_eq.cpt -o 1tsk_sim
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Ignoring obsolete mdp entry 'optimize-fft'
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Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
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Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'
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Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
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NOTE 1 [file sim.mdp]:
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  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
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Setting the LD random seed to 917544437
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Generated 2556 of the 2556 non-bonded parameter combinations
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Generating 1-4 interactions: fudge = 0.5
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Generated 2556 of the 2556 1-4 parameter combinations
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Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
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turning all bonds into constraints...
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turning all bonds into constraints...
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turning all bonds into constraints...
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Excluding 1 bonded neighbours molecule type 'SOL'
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Excluding 1 bonded neighbours molecule type 'CL'
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Cleaning up constraints and constant bonded interactions with virtual sites
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Removing all charge groups because cutoff-scheme=Verlet
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Analysing residue names:
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There are:    35    Protein residues
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There are:  3929      Water residues
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There are:     5        Ion residues
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Analysing Protein...
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Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
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Number of degrees of freedom in T-Coupling group System is 24617.00
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Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 160 K
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Reading Coordinates, Velocities and Box size from old trajectory
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Will read whole trajectory
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Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm
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Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
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Note that mdrun will redetermine rlist based on the actual pair-list setup
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Last frame         -1 time  100.000   
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Using frame at t = 100 ps
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Starting time for run is 0 ps
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Calculating fourier grid dimensions for X Y Z
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Using a fourier grid of 42x42x42, spacing 0.115 0.115 0.115
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Estimate for the relative computational load of the PME mesh part: 0.18
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NOTE 2 [file sim.mdp]:
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  This run will generate roughly 40654 Mb of data
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There were 2 notes
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Back Off! I just backed up 1tsk_sim.tpr to ./#1tsk_sim.tpr.2#
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GROMACS reminds you: "Interfacing Space and Beyond..." (P. J. Harvey)
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