[gmx-users] restore pbc after a rotation

[Tsjerk Wassenaar]

Hi Xavier,

By when do you need it? You can send me one frame ( .gro) and I can
see what I can do. But no guarantees, and no time indication :(

Cheers,

Tsjerk

On Mon, Jan 26, 2009 at 7:11 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> 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
>> P: +31-30-2539931
>> F: +31-30-2537623
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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