[gmx-users] restore pbc after a rotation

[Tsjerk Wassenaar]

Hi XAvier,

Unfortunately, you're out of luck. The coordinates do not contain
information regarding the proper orientation with respect to the
coordinate system.

That's the short answer. I guess you did save all atoms, at least of
proteins and lipids, in which case you could do a search for a
rotation matrix  that restores your PBC. If you have a brick or
triclinic representation of your atoms the easiest solution is to fit
planes through the sides, from which you can infer the original
coordinate system. Then you can rotate that back to match the one
stored.

Hope it helps,

Tsjerk

On Sun, Jan 25, 2009 at 7:43 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> Dears,
>
> I need to rerun a trajectory that has been rotated to orient a molecule
> according to a reference. The pbc are therefore broken.
>
> Would anyone know how to restore the correct position of the atoms inside
> the unit cell after the rotation is applied. The rotation is actually
> applied around
> only one axis (z, membrane normal).
>
> Thanks for any suggestion.
> XAvier.
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623