[gmx-developers] trjconv defaults

Erik Lindahl lindahl at cbr.su.se
Fri Oct 17 12:01:58 CEST 2008


On Oct 17, 2008, at 11:44 AM, Berk Hess wrote:

> 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.

Yes, it works, but you have to process the trajectory 2-3 times to  
first get the protein whole, then remove translation, and finally get  
the water in the box ;-)



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