[gmx-users] Dummies usage doubts

[David van der Spoel]

Jones de Andrade 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?
> 
no time. but start by adding one dummy at a time run EM and check 
whether they end up in the same place.


> 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 
> <mailto: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
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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-- 
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