[gmx-users] grompp 4.0.5 hangs while 3.2.1 works

Kaihsu Tai k at kauha.eu
Thu May 21 17:07:03 CEST 2009

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
-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

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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