[gmx-developers] trjconv defaults

Berk Hess hessb at mpip-mainz.mpg.de
Fri Oct 17 11:00:40 CEST 2008


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.


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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