AMBER Archive (2004)

Subject: AMBER: ptraj bug?

From: Ian Withers (
Date: Wed May 19 2004 - 09:33:38 CDT

Dear Amber users,

I am attempting to use ptraj to perform PCA analysis, and in particular
to use the eigenvector matrix to create animations of the motion of
proteins projected onto each mode. The problem I have is that the output
file created by the analyze matrix command with the option "vecs 3*N"
upon a 3*N by 3*N covariance matrix (N is the number of atoms being
considered) only contains only 3*N-1 eigenvectors!
Is this a bug in the analyze matrix function of ptraj?

Thanks in advance,

Dr. Ian Withers                Tel: +44 (0)115 8468009
Centre for Biomolecular Science,
University of Nottingham,      email:
Nottingham, NG7 2RD, UK.

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