Re: [AMBER-Developers] [AMBER] Visualizing ptraj eigenvectors

From: B. Lachele Foley <>
Date: Tue, 22 May 2012 14:04:09 +0000

Ha! I finally gave up on the VMD plugin years ago and used gnuplot. Not the most amazing molecule visualization program, but at least it worked.

I can't be much help, but will second and applaud anyone who takes a stab at making it work.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: David A. Case []
Sent: Tuesday, May 22, 2012 6:59 AM
Subject: Re: [AMBER-Developers] [AMBER] Visualizing ptraj eigenvectors

On Tue, May 22, 2012, wrote:

> I am trying to compute PCA-eigenvectors from an MD trajectory and would
> like to visualize them.
> So I do something like:
> {read and rmsfit trajectory}
> matrix covar name m1 .CA
> analyze matrix m1 vecs vecs.out
> analyze modes displ file vecs.out out displ.out
> Now, if I'm not mistaken, displ.out will contain the coordinate changes
> that I would like to visualize, but how do I load them into e.g. VMD? I
> know the IED program from UCSD could show amber vectors, but it's fickly
> to install and I wondered if there is a more recent option to do that.

Re-directing to Amber-developers: it would be great if difficulties with IED
could be resolved, most likely by someone who wants the solution. There are
some improvements beyond installation needed, mainly in having a nice
interface to control the visual amplification of the modes. I'll see if an
undergrad with python experience can look at this, but anyone else is free to
jump in.


AMBER-Developers mailing list

AMBER-Developers mailing list
Received on Tue May 22 2012 - 07:30:03 PDT
Custom Search