[gmx-users] restore pbc after a rotation

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 26 12:58:11 CET 2009

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

Hope it helps,


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.
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

More information about the gromacs.org_gmx-users mailing list