AMBER Archive (2004)

Subject: Re: AMBER: ptraj bug?

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed May 19 2004 - 10:31:12 CDT

Ian Withers schrieb:
>
> 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?

It's not a bug, it's more a "feature" of the arpack routine "dsaupd"
used in ptraj to calculate eigenvalues/eigenvectors in an iterative
manner. The reason why this routine was chosen is that in most cases it
suffices (and is faster than diagonalizing the whole matrix) to
calculate the first few eigenvectors to get the information on the
"essential dynamics" of a protein. If you really need the very last
eigenvector, you may want to take a look into the analyzeMatrix function
in analyze.c in the $AMBERHOME/src/ptraj directory.

Best regards

Holger

>
> Thanks in advance,
> Ian
>
> --
> Dr. Ian Withers Tel: +44 (0)115 8468009
> Centre for Biomolecular Science,
> University of Nottingham, email: ianw_at_holmes.cancres.nottingham.ac.uk
> Nottingham, NG7 2RD, UK. http://holmes.cancres.nottingham.ac.uk/mrg/ianw/
>
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++                             
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
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