[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?

[Tsjerk Wassenaar]

Hi Lin,

You don't get such axes directly from covariance analysis. If you want
to know which rotations are associated with a certain eigenvector, you
have to run a routine like dyndom (http://fizz.cmp.uea.ac.uk/dyndom/)
on the extreme projections of your trajectory onto an eigenvector.

Cheers,

Tsjerk

On Fri, May 27, 2011 at 4:54 AM, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
>
> Hi
> I want to protein's domain motion.
> I use   g_covar    and    g_anaeig  to get the eigenvectors.
> How can i get the rotational axis of which protein do its domain motion from
> those eigenvectors?
> I found the papers and the authors plot its rotational axis of domain
> motion.
> How did they make it ?
>
> Thank you
> Lin
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands