AMBER Archive (2007)Subject: AMBER: iRED and corrired
From: Francois Theillet (ftheille_at_pasteur.fr)
Date: Fri Feb 02 2007  11:07:47 CST
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 n1 eigenvectors (and eigenvalues) instead of the hoped n.
The sum of the eigenvalues is not exactly equal to n, but around
nlambda(n1) (with lamda(n1) the associated eigenvalue of the n1th
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 n1 eigenvectors)
Consequently the following timecorrelation evaluation treats only n1
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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