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 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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu