AMBER Archive (2006)

Subject: Re: AMBER: Mass wieghted Covariance Matrix

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Apr 12 2006 - 02:46:19 CDT

Am Mittwoch, 12. April 2006 09:16 schrieb Daniel Oehme:
> Dear AMBER Community,
>
> A quick question about Entropy analysis with ptraj. When calculating a
> mass weighted covariance matrix the following is output to the ptraj
> output file.
>
> 7> MATRIX: Calculating mass weighted covar matrix by atom using no
> mass weighting
>
>
> Why would mass weighted covariance matrix be calculated without mass
> weighting? I have seen this in a few other postings where people have
> been doing entropy calculations so I know it is not just an isolated
> incident.

I admit the output is a little confusing. So the first "mass weighted" refers
to the covar matrix, i.e., the matrix is calculated as requested. The second
"mass weighting" refers to the output option for the matrix, which is "by
atom" in this case (the only valid option for a mass-weighted covar matrix).
For other matrices (see Amber manual), byres or bymask output will also be
possible. In these cases, the calculated averages can be calculated "in a
normal way" or "mass-weighted". Bottom line: the "using no mass weighting"
doesn't make much sense here, but it does not affect the calculation you
intend either.

Best regards

Holger

>
> Daniel Oehme
> PhD Student, La Trobe University
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universitaet
Fachbereich Biowissenschaften
Institut für Zellbiologie und Neurowissenschaft
Max-von-Laue-Str. 9
60438 Frankfurt/Main
Germany

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29527
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
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