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From: Francois Theillet <ftheille.pasteur.fr>

Date: Fri, 02 Feb 2007 18:07:47 +0100

Dear AMBER users (or developpers...),

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)

Consequently the following timecorrelation evaluation treats only n-1

modes instead of n modes.

So, in my opinion, it lacks the last eigenvector (which corresponds to

the smaller eigenvalue).

But, there is maybe another problem, which could be for instance a

misunderstanding from me of the iRED method...

Does anybody have got an idea about this situation ?

Thanks,

François Theillet

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Received on Sun Feb 04 2007 - 06:07:57 PST

Date: Fri, 02 Feb 2007 18:07:47 +0100

Dear AMBER users (or developpers...),

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)

Consequently the following timecorrelation evaluation treats only n-1

modes instead of n modes.

So, in my opinion, it lacks the last eigenvector (which corresponds to

the smaller eigenvalue).

But, there is maybe another problem, which could be for instance a

misunderstanding from me of the iRED method...

Does anybody have got an idea about this situation ?

Thanks,

François Theillet

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Received on Sun Feb 04 2007 - 06:07:57 PST

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