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

From: Mark Williamson <>
Date: Wed, 23 May 2012 10:22:05 +0100

On 22/05/12 11:59, David A. Case wrote:
> 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.

Hi Dave,

I recently produced a mini-how to on getting VMD to work with IED,
please see the PDF attached. If there are any issues, please let me know.



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Received on Wed May 23 2012 - 02:30:04 PDT
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