[gmx-users] Dummies usage doubts

[Jones de Andrade]

Hi all.

Just informing, I tried a single molecule, and the topology with all dummies
minimize (despite taking loads of steps bfgs steps).

The interesting thing is that the distance between atom 6 and 17 at
beggining reads 3.1 angstrons, and at the end read 2.9 angstrons.

Why it's going bad with many molecules or even single molecule MD, God?

Thanks a lot everybody in advance,

Sincerally yours,

Jones

On 10/11/07, Jones de Andrade <johannesrs at gmail.com> wrote:
>
> 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
> this?
>
> I'll run a single molecule now.
>
> Thanks a lot in advance,
>
> Sincerally yours,
>
> Jones
>
> 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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