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

From: David A. Case <>
Date: Tue, 22 May 2012 06:59:35 -0400

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.


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Received on Tue May 22 2012 - 04:00:03 PDT
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