[gmx-developers] trjconv defaults

[Berk Hess]

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.

Berk