[gmx-developers] Heads up! trjconv broken

[Daniel Larsson]

On Jun 14, 2010, at 18:56 , Tsjerk Wassenaar wrote:

> 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,

Yes, the settings that I've tried now that causes the unexpected behavior do all involve the -fit flag.

So, if I understand this correctly: -fit with either rot+trans, rotxy+transxy or progressive will/might not wrap atoms that passes a periodic boundary "correctly".

This is not something that was obvious to me, and I think it might be good to add a note about this in the documentation as a service to the user. Perhaps trjconv should even disallow any PBC flag together with these above options? And perhaps also display a warning in conjunction with the use of these flags (since one can have made multiple passes over a trajectory).

Thanks for helping me out Tsjerk!

> 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
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