[gmx-users] Dummies usage doubts

[Jones de Andrade]

Hi all.

Ok, I found the erors. One small in the topology, and another huge in the
.gro formating.

I'll deal with a few other molecules in the next days, and hopefully I'll be
able to make a small contribution to the programs library with a little
"add_dummies" program.

Will test it a bit more, though.

Anyway, thanks a lot everybody for all help!  :)

Sincerally yours,

Jones

On 10/11/07, Jones de Andrade <johannesrs at gmail.com> wrote:
>
> 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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