AMBER Archive (2006)

Subject: Re: AMBER: Cosine content calculation

From: Hannes Loeffler (
Date: Thu Mar 09 2006 - 19:02:48 CST

On Thu, 09 Mar 2006 11:01:20 +0100
"matteo filandri" <> wrote:

> Excuse me but in the paper cited, and in the Hess formula (Hess B,
> Physical Review E vol 62, n°6,pp8438), lambda is not the wavelenght
> but the eigenvalue (nm^2).
> In a few words, I need the eigenvalue expressed as in the NO
> mass-weighted matrix (nm^2)

If you need the non mass-weighted matrix then I guess you should use
ptraj with
matrix covariance
which generates the variance-covariance matrix from cartesian
coordinates. The eigenvalues should then be in Angstrom squared.


Hannes Loeffler | tel: +81-3-5841-1472 | fax: +81-3-5841-2297 | mailto:hal->iam u-tokyo ac jp
Laboratory of Molecular Design, Center of Bioinformatics, Institute of
Molecular and Cellular Biosciences, The University of Tokyo, Japan
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