Re: AMBER: iRED and corrired

Date: Sun, 04 Feb 2007 14:01:17 +0100

Hi,

we have been looking into the iRED part recently. We have also changed
it such that now all eigenvectors/values are available (among other
things). I will prepare a patch on Monday and distribute it.

Best regards

Holger

Quoting "David A. Case" <case.scripps.edu>:

> 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:
>
> http://amber.ch.ic.ac.uk/archive/200501/0154.html
>
> 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.
> 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 Wed Feb 07 2007 - 06:07:06 PST
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