RE: [AMBER] PCA analysis with ptraj

From: Alessandro Contini <alessandro.contini.unimi.it>
Date: Tue, 10 Nov 2009 13:03:48 +0100

Thank you, that's what I did but I wasn't sure about the "correctness"
of the operation.

Thanks again, best regards

Alessandro

Il giorno mar, 10/11/2009 alle 08.13 +0000, hannes.loeffler.stfc.ac.uk
ha scritto:
> > 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.
>
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Received on Tue Nov 10 2009 - 04:30:02 PST
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