AMBER Archive (2009)

Subject: RE: [AMBER] PCA analysis with ptraj

Date: Tue Nov 10 2009 - 02:13:29 CST

> However, I didn't found a tool or a command to
> allow the calculation of the contribution of each eigenvector to the
> total motion of my system.

You simply compare the eigenvalue (=variance along the correpsonding mode)
of interest with the sum of all eigenvalues (you can get the same value
from the sum of diagonal elements of the matrix).

> (i.e. I don't see 3N rows and 3N lines).

Well, it might not be stored in that way but if you sum up all entries you
will arrive at 3N X 3N.

-- Scanned by iCritical.

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