Re: AMBER: iRED and corrired

From: David A. Case <>
Date: Fri, 2 Feb 2007 10:57:43 -0800

On Fri, Feb 02, 2007, Francois Theillet wrote:
> I have a problem with the treatment of the iRED method in ptraj (AMBER 8):
> I have a system of n vectors (i.e. a nxn covariance matrix), and I
> obtain only n-1 eigenvectors (and eigenvalues) instead of the hoped n.
> The sum of the eigenvalues is not exactly equal to n, but around
> n-lambda(n-1) (with lamda(n-1) the associated eigenvalue of the n-1th
> eigenvector).
> (I tried several n, the result is identical. If I precise that I want k
> eigenvectors (k<n), I obtain the first k eigenvectors correctly. With
> k>n, I obtain n-1 eigenvectors)

This question (I think) has come up before:

The ptraj code uses an arpack routine to compute eigenvalues/vectors, which
seems to be limited to n-1 results. For PCA analysis, this is not really a
limitation; I'm not sure whether the same is true for iRED or not. Please let
us know if you really need that last eigenvector: we can put it on a list of
things to look at in the next round of ptraj updates.

...thanks for the report....dac

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Received on Sun Feb 04 2007 - 06:08:00 PST
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