[gmx-users] grompp 4.0.5 hangs while 3.2.1 works

[Berk Hess]

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: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> 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...
> > 
> > _______________________________________________
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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.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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