[gmx-users] rotational fit in XY plane only

Bert de Groot bgroot at gwdg.de
Wed May 2 14:16:35 CEST 2007

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 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

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