Re: [AMBER] PCA and motions visualization

From: Jason Swails <>
Date: Tue, 21 Jul 2015 12:20:20 -0400

On Tue, Jul 21, 2015 at 5:59 AM, <> wrote:

> Dear amber user's
> I would like to visualize the result of the pca analyses on my
> trajectories.
> Following instructions founded at this tutorial :
> i was able to produce the covariance matrix and then to compute the
> eigenvector and the eigenvalue. I have obtained that the first two
> eigenvectors share the 70% of the information.
> I have projected the trajectory along the first two PCs obtaining a file
> with mode1 and mode2.
> I this point I would like to visualize the protein movements for both
> the PCs.

​Then it sounds like what you want is to create a "pseudo-trajectory" along
each of those modes.

This is supported by the modes command that you used below. Just add a
"trajout" argument to it. See page 616 of the Amber 15 manual, with an
example of writing a pseudo-trajectory on page 617.

> center origin :1-982
> image origin center

​I strongly suggest replacing these two commands with the single command


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jul 21 2015 - 09:30:02 PDT
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