[gmx-users] ED analysis

Berk Hess gmx3 at hotmail.com
Mon Sep 6 13:36:09 CEST 2004

>From: Ruben M Buey <ruben at akilonia.cib.csic.es>
>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] ED analysis
>Date: Mon, 06 Sep 2004 13:13:05 +0200
>Hi all,
>Just a novice´s question about ED analysis.
>What does it mean when I get a nice correlation between the projections 
>onto the eigenvectors 1 and 2 of a MD trajectory?
>Actually the graph has a pretty semi-circumference shape... when I look at 
>the extreme projections over these eigenvectors, I can only see really 
>small diferences between the structures but no domain movements or 
>collective motions. How can I look at this?

A typical case of very incomplete sampling.
You are only seeing small diffusive motion in eigenvectors 1 and 2.
See covariance analysis in the manual and the references given
in that section.


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