[gmx-users] grompp 4.0.5 hangs while 3.2.1 works

David van der Spoel spoel at xray.bmc.uu.se
Thu May 21 23:55:32 CEST 2009

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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