[gmx-users] Periodic boundary problem

[Kay Gottschalk]

did you try trjconv -pbc cluster?

On Nov 4, 2004, at 11:14 AM, Haberl Florian wrote:

> dear gmx-users,
>
> I want to perform an md simulation with an dimer proteine.
> after performing em/pr/ or md the dimer is seperated in
> two monomers and one of this is outside my waterbox
> (viewed by gopenmol).
>
> After some search i found the trjconv command should fix this
> problem which is caused through periodic boundary conditions
> (i guess this is the problem).
>
> So an -pbc nojump should fix it, but this is not always so,
> sometimes it^s still outside the box and i don^t know why.
>
> Tried this now with several input files but always same behavoir.
>
> Any suggests how to fix this?
>
>
> Greetings,
>
> Florian
>
>
> ----------------------------------------------------------------------- 
> -
>  Florian Haberl              Universitaet Erlangen/Nuernberg
>  Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
>
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
>
> ----------------------------------------------------------------------- 
> -
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>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
Rehovot
Israel
+972-8-934 3639