[gmx-users] restore pbc after a rotation

[XAvier Periole]

Hi Tsjerk,

There is no rush and I really can use the copies of the box.

But as you insist I'll send you the gro file off list.

XAvier.

On Jan 26, 2009, at 9:06 PM, Tsjerk Wassenaar wrote:

> 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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>>
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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
> _______________________________________________
> 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 the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php