[gmx-developers] trjconv defaults

Berk Hess hessb at mpip-mainz.mpg.de
Fri Oct 17 11:44:40 CEST 2008

David van der Spoel wrote:
> Erik Lindahl wrote:
>> Hi,
>> I agree with Berk here.
> OK, fine.
>> Another (unrelated) problem occurs when we write e.g. large ion 
>> channels with multiple chains - it can be quite nasty to get the 
>> chains in the same periodic image without using the clustering 
>> option, which right now is horribly slow for large systems...
> Doesn't -pb mol combined with centering do the trick?
I would say -pbc nojump is the magic option that fixes all this at one 
and it fast,
only the solvent will then move out of the box over time.


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