[gmx-developers] Heads up! trjconv broken

[Tsjerk Wassenaar]

Hi Daniel,

-fit and -pbc should not be combined, and -pbc should never follow a
call with -fit. Note that fit rotates the coordinates with respect to
the box, breaking the relation with the PBC. Then think whether the
mangling you see follows logically from this, or not, in which case it
might actually be a bug. But at this point, I doubt it.

Cheers,

Tsjerk

On Mon, Jun 14, 2010 at 6:49 PM, Daniel Larsson <larsson at xray.bmc.uu.se> wrote:
> Be very careful to delete original trajectories after using trjconv to de-convolute complex box types such as rhombic dodecahedrons.
>
> I have yet to figure out the exact combinations that causes the misbehavior, but from what I have experienced so far a rhombic dodecahedron box in some combinations with the -pbc, -ur, -fit and -center flags severely mangles the coordinates so that e.g. water molecules ends up in completely wrong places.
>
> I'll work out how to reproduce the bug and file a bugzilla.
>
> - Daniel
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands