[gmx-users] rotational fit in XY plane only

[Bert de Groot]

Berk Hess wrote:
> 
> 
> 
>> From: Dr Itamar Kass <ikass at uq.edu.au>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: [gmx-users] rotational fit in XY plane only
>> Date: Wed, 02 May 2007 19:44:12 +0800
>>
>> Hi all,
>>
>> I study a protein which is moving toward an interface during my
>> simulation. In order to analyse the why the protein is bound to the
>> interface I want to fit all my results. There is no problem with
>> translational fit, but I want to do rotational fit only in the XY plane.
>> Is there a nice way of doing so?
>>
>> Best,
>> Itamar
> 
> Currently there is not.
> I would like to have that feature as well.
> 

can't you simply set all z-coordinates to zero and carry out a 3D fit as usual?
(you may get a problem with mirror images, but the handedness is anyway not
anymore uniquely defined once you project on 2D).


Bert

______________________________________
Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302
http://www.mpibpc.mpg.de/groups/de_groot