[gmx-users] Polarisable water

Michael Bajomo bajomo at gmail.com
Thu Dec 1 15:13:57 CET 2005

Hi Guys,

Sorry for being sketchy on the details. I was trying to merge an unpolarised
water topology file with a polarised one (sw3.itp....similar to sw.itp in
gromacs). I am essentially repeating the Ribonuclease S -peptide tutorial in
the "getting started" section of the gromacs website (but with polarisable
water). When I preprocess the modified topology file (inorder to do energy
minimization...em) in grompp   *(**grompp -v -f em -c b4em -o em -p
speptide) *I get the following output*:*

                  *       :-)  G  R  O  M  A  C  S  (-:

                              S  C  A  M  O  R  G

                             :-)  VERSION 3.3  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2004, The GROMACS development team,
            check out **http://www.gromacs.org*
<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.

                    :-)  /usr/local/gromacs/bin/grompp  (-:

Option     Filename  Type         Description
  -f         em.mdp  Input, Opt!  grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c       b4em.gro  Input        Generic structure: gro g96 pdb tpr tpb tpa

  -r       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
 -rb       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa

  -n      index.ndx  Input, Opt.  Index file
-deshuf  deshuf.ndx  Output, Opt. Index file
  -p   speptide.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o         em.tpr  Output       Generic run input: tpr tpb tpa xml
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj
  -e       ener.edr  Input, Opt.  Generic energy: 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.
         -np    int      1  Generate statusfile for # nodes
-[no]shuffle   bool     no  Shuffle molecules over nodes
   -[no]sort   bool     no  Sort molecules according to X coordinate
-[no]rmvsbds   bool    yes  Remove constant bonded interactions with virtual

       -load string         Releative load capacity of each node on a
                            parallel machine. Be sure to use quotes around
                            the string, which should contain a number for
                            each node
    -maxwarn    int     10  Number of warnings after which input processing
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals
  -[no]renum   bool    yes  Renumber atomtypes and minimize number of

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.81#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Cleaning up temporary file gromppaew5iO
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 754

Fatal error:
Atoms in the .top are not numbered consecutively from 1*
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