[gmx-users] Gromacs version for polarizable model
Mark Abraham
mark.j.abraham at gmail.com
Wed Jun 22 09:50:48 CEST 2016
Hi,
Don't know. Try 5.1.2.
Mark
On Wed, Jun 22, 2016 at 9:12 AM Luca Banetta <luca.banetta at gmail.com> wrote:
> NNODES=1, MYRANK=0, HOSTNAME=compute-0-2.local
> :-) G R O M A C S (-:
>
> Grunge ROck MAChoS
>
> :-) VERSION 4.5.4 (-:
>
> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
> Berk Hess, David van der Spoel, and Erik Lindahl.
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2010, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> This program is free software; you can redistribute it and/or
> modify it under the terms of the GNU General Public License
> as published by the Free Software Foundation; either version 2
> of the License, or (at your option) any later version.
>
> :-) mdrun (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -s topol.tpr Input Run input file: tpr tpb tpa
> -o traj.trr Output Full precision trajectory: trr trj cpt
> -x traj.xtc Output, Opt. Compressed trajectory (portable xdr
> format)
> -cpi state.cpt Input, Opt. Checkpoint file
> -cpo state.cpt Output, Opt. Checkpoint file
> -c confout.gro Output Structure file: gro g96 pdb etc.
> -e ener.edr Output Energy file
> -g md.log Output Log file
> -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
> -field field.xvg Output, Opt. xvgr/xmgr file
> -table table.xvg Input, Opt. xvgr/xmgr file
> -tablep tablep.xvg Input, Opt. xvgr/xmgr file
> -tableb table.xvg Input, Opt. xvgr/xmgr file
> -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
> -tpi tpi.xvg Output, Opt. xvgr/xmgr file
> -tpid tpidist.xvg Output, Opt. xvgr/xmgr file
> -ei sam.edi Input, Opt. ED sampling input
> -eo sam.edo Output, Opt. ED sampling output
> -j wham.gct Input, Opt. General coupling stuff
> -jo bam.gct Output, Opt. General coupling stuff
> -ffout gct.xvg Output, Opt. xvgr/xmgr file
> -devout deviatie.xvg Output, Opt. xvgr/xmgr file
> -runav runaver.xvg Output, Opt. xvgr/xmgr file
> -px pullx.xvg Output, Opt. xvgr/xmgr file
> -pf pullf.xvg Output, Opt. xvgr/xmgr file
> -mtx nm.mtx Output, Opt. Hessian matrix
> -dn dipole.ndx Output, Opt. Index file
> -multidir rundir Input, Opt., Mult. Run directory
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -[no]version bool no Print version info and quit
> -nice int 0 Set the nicelevel
> -deffnm string Set the default filename for all file options
> -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
> -[no]pd bool no Use particle decompostion
> -dd vector 0 0 0 Domain decomposition grid, 0 is optimize
> -npme int -1 Number of separate nodes to be used for PME, -1
> is guess
> -ddorder enum interleave DD node order: interleave, pp_pme or
> cartesian
> -[no]ddcheck bool yes Check for all bonded interactions with DD
> -rdd real 0 The maximum distance for bonded interactions
> with
> DD (nm), 0 is determine from initial
> coordinates
> -rcon real 0 Maximum distance for P-LINCS (nm), 0 is
> estimate
> -dlb enum auto Dynamic load balancing (with DD): auto, no or
> yes
> -dds real 0.8 Minimum allowed dlb scaling of the DD cell size
> -gcom int -1 Global communication frequency
> -[no]v bool no Be loud and noisy
> -[no]compact bool yes Write a compact log file
> -[no]seppot bool no Write separate V and dVdl terms for each
> interaction type and node to the log file(s)
> -pforce real -1 Print all forces larger than this (kJ/mol nm)
> -[no]reprod bool no Try to avoid optimizations that affect binary
> reproducibility
> -cpt real 15 Checkpoint interval (minutes)
> -[no]cpnum bool no Keep and number checkpoint files
> -[no]append bool yes Append to previous output files when continuing
> from checkpoint instead of adding the
> simulation
> part number to all file names
> -maxh real -1 Terminate after 0.99 times this time (hours)
> -multi int 0 Do multiple simulations in parallel
> -replex int 0 Attempt replica exchange every # steps
> -reseed int -1 Seed for replica exchange, -1 is generate a
> seed
> -[no]ionize bool no Do a simulation including the effect of an
> X-Ray
> bombardment on your system
>
>
> Back Off! I just backed up md.log to ./#md.log.1#
> Reading file topol.tpr, VERSION 4.5.4 (single precision)
>
> Back Off! I just backed up traj.trr to ./#traj.trr.1#
>
> Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
>
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
>
> WARNING: This run will generate roughly 29462 Mb of data
>
> starting mdrun 'mixture'
> 1000000 steps, 100.0 ps.
> --
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