[gmx-users] multiple T-Coupling groups

simon sangma simoniitchem at gmail.com
Fri Aug 28 16:11:18 CEST 2009

    I used the followng command and encountered an error. Can someone please
offer a solution.
grompp -f grompp.mdp -n index.ndx -p topl.top -c conf.gro -o water.tpr
                           :-)  G  R  O  M  A  C  S  (-:
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                            :-)  VERSION 4.0.4  (-:

      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     grompp.mdp  Input, Opt!  grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c       conf.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      topol.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o      water.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
-[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'
Ignoring obsolete mdp entry 'domain-decomposition'
Replacing old mdp entry 'unconstrained-start' by 'continuation'

WARNING 1 [file grompp.mdp, line unknown]:
  Unknown or double left-hand 'zero-temp_time' in parameter file

checking input for internal consistency...

WARNING 2 [file grompp.mdp, line unknown]:
  epsilon_r = 0 and epsilon_rf = 1 with reaction field, assuming old format
  and exchanging epsilon_r and epsilon_rf

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...

Program grompp, VERSION 4.0.4
Source code file: readir.c, line: 1058

Fatal error:
Atom 1 in multiple T-Coupling groups (1 and 2)

"Wild Pointers Couldn't Drag Me Away" (K.A. Feenstra)
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