[gmx-developers] trjconv defaults

[Berk Hess]

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,