[gmx-users] Dummies usage doubts

Jones de Andrade johannesrs at gmail.com
Thu Oct 11 18:52:11 CEST 2007

Hi Prof. David.

Yes, it a self created topology. This one is based on another self created
topology that runs perfectly for cyclohexane. It was adapted to include the
dummy atoms.

I guess there is something wrong in the definition of the dummies in the
topology. But I have no clue where it is. Can you provide me some clue on

I'll run a single molecule now.

Thanks a lot in advance,

Sincerally yours,


On 10/11/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Jones de Andrade wrote:
> > Hi Prof. David.
> >
> > What details do you mean? Actual topology files are attached. Anything
> else?
> >
> > Thanks a lot in advance!
> >
> > Sincerally yours,
> >
> > Jones
> >
> There is something wrong in the topology, youäll have to debug it
> yourself...
> --
> David van der Spoel, Ph.D.
> 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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