Re: [AMBER] Modes associated to the principal components?

From: David A Case <>
Date: Tue, 22 Nov 2016 14:00:16 -0500

On Tue, Nov 22, 2016, The Cromicus Productions wrote:

> I'm able to compute the principal components of a given trajectory using
> PCAsuite.
> Then, I can convert them into pdb files and watch the motions.
> PCAsuite also gives me the eigenvalues, so I know which are the most
> important.
> Now, if I understand correctly, the principal components are some "chosen"
> normal modes which summarize the information of the trajectory, but how do
> I know which normal mode is associated to each component I get? In
> particular, I would like to know what is the associated vibration frequency
> of each of the components.

You should read about quasiharmonic analysis, which is a (trivial) variant of
PCA analysis. Might as well start here:

%A M. Karplus
%A J.N. Kushick
%T Method for estimating the configurational entropy of macromolecules
%J Macromolecules
%V 14
%P 325-332
%D 1981

Although the method is also described in lots of textbooks and review
articles. cpptraj can compute both.

Note that, speaking strictly, none of these are true "normal modes".


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Received on Tue Nov 22 2016 - 11:30:02 PST
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