[gmx-users] restore pbc after a rotation

[XAvier Periole]

On Jan 26, 2009, at 12:58 PM, Tsjerk Wassenaar wrote:

> Hi XAvier,
>
> Unfortunately, you're out of luck. The coordinates do not contain
> information regarding the proper orientation with respect to the
> coordinate system.
No they don't.

May be I should have mentioned that I know for each
conformation of the system (protein embedded in a membrane
bilayer) the exact transformation that has been that has
been operated: a rotation around the z axis.
>
> 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.
The other option I found is to duplicate the system on x and y
directions, then center a copy of the protein and finally put everything
inside the new cell (made up from 4 copies of the original cell).
Then when rotating the pbc and included on the x and y directions.

Thanks for you thoughts I knew you'd had but I hope for a magic
solution.

Best,
XAvier
>
> 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
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