[gmx-users] covariance

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 19 15:14:55 CET 2009

Hi Morteza,

Your question suggests a lack of understanding of the principles (not
principals) of covariance analysis. It is probably best to read a bit
more on the background of this technique, until you realize what it
is, what it can do, and what it can't. There are a number of
discussions archived on the matter. I also briefly touch the topic in
the tutorial at http://nmr.chem.uu.nl/~tsjerk/course/molmod/
(analysis). But the best references to get to understand the technique
are probably from statistics. Googling will yield plenty of documents.
If you feel that I'm off with this reply, then please give a more
detailed account of what you intend to do and how you think covariance
analysis will help you achieving your aim.

Hope it helps,


2009/11/19 Morteza Khabiri <khabiri at greentech.cz>:
> Dear gmxuser
> I want to compare a dimer covariance which was already run in 2 different
> situation. The problem is that the scale of produced covariance (which
> produced by -xpma) in 2 case is different e.g the scale for one of them
> start from -0.18 to 0.05 and other -0.15 to 0.052. Is there any
> possibility to calculate covarianse in the same scale?
> thanks
> --
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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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