Hi,
You have an error in your input file.
Does grompp also hang with correct mdp parameters?
Berk
> Date: Thu, 21 May 2009 23:55:32 +0200
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] grompp 4.0.5 hangs while 3.2.1 works
>
> Kaihsu Tai wrote:
> > I have a system which works with grompp 3.2.1 but grompp
> > 4.0.5 hangs at ‘processing topology...’. Is there something
> > that had changed (say, file format in .top or .itp) that
> > could have caused this? I can supply my topology,
> > conformation, etc. files if necessary for debugging. Cheers.
> >
> > $ grompp -v -f test0_.mdp -po test0.mdp -c initial.gro -p Kir21.top -o
> > test0.tpr
> > :-) G R O M A C S (-:
> >
> > GROwing Monsters And Cloning Shrimps
> >
> > :-) VERSION 4.0.5 (-:
> >
> >
> > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > Copyright (c) 2001-2008, The GROMACS development team,
> > 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.
> >
> > :-) grompp (-:
> >
> > Option Filename Type Description
> > ------------------------------------------------------------
> > -f test0_.mdp Input, Opt! grompp input file with MD parameters
> > -po test0.mdp Output grompp input file with MD parameters
> > -c initial.gro Input Structure file: gro g96 pdb tpr tpb tpa
> > -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> > -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> > -n index.ndx Input, Opt. Index file
> > -p Kir21.top Input Topology file
> > -pp processed.top Output, Opt. Topology file
> > -o test0.tpr Output Run input file: tpr tpb tpa
> > -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> > -e ener.edr Input, Opt. Energy file: edr ene
> >
> > Option Type Value Description
> > ------------------------------------------------------
> > -[no]h bool no Print help info and quit
> > -nice int 0 Set the nicelevel
> > -[no]v bool yes Be loud and noisy
> > -time real -1 Take frame at or first after this time.
> > -[no]rmvsbds bool yes Remove constant bonded interactions with virtual
> > sites
> > -maxwarn int 0 Number of allowed warnings during input
> > processing
> > -[no]zero bool no Set parameters for bonded interactions without
> > defaults to zero instead of generating an error
> > -[no]renum bool yes Renumber atomtypes and minimize number of
> > atomtypes
> >
> > Ignoring obsolete mdp entry 'title'
> > Ignoring obsolete mdp entry 'cpp'
> >
> > Back Off! I just backed up test0.mdp to ./#test0.mdp.7#
> > checking input for internal consistency...
> >
> > NOTE 1 [file test0_.mdp, line unknown]:
> > The Berendsen thermostat does not generate the correct kinetic energy
> > distribution. You might want to consider using the V-rescale thermostat.
> >
> >
> > ERROR: With coulombtype = PME, rcoulomb must be equal to rlist
> > If you want optimal energy conservation or exact integration use PME-Switch
> >
> > processing topology...
> >
> > _______________________________________________
> > gmx-users mailing list [email protected]
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> Please submit a bugzilla with all input files to reproduce the problem.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> [email protected] [email protected] http://folding.bmc.uu.se
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