[gmx-developers] trjconv defaults

Erik Lindahl lindahl at cbr.su.se
Fri Oct 17 11:16:37 CEST 2008


I agree with Berk here.

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...



On Oct 17, 2008, at 11:00 AM, Berk Hess wrote:

> Hi,
> It would be nice to somehow automatically have trjconv fix molecules,
> but there are several issues.
> 1) trjconv will then by default need a tpr file
> 2) for trajectory conversion you don't want this in general
> (automatically modifies your trajectories and makes things slower)
> I think that ideally trjconv should do -pbc mol automatically when  
> writing
> pdb or gro. But that is confusing, since the settings of options  
> will then
> depends on  the output format.
> Berk
> David van der Spoel wrote:
>> Hi,
>> shall we set the trjconv defaults to -pbc mol -ur compact ?
>> Even I get fooled when dumping a pdb file and suddenly noticing  
>> that it is broken.
>> Cheers,
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