[gmx-users] covariance

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 19 16:30:56 CET 2009

Hi Morteza,

To me, your initial question seemed to relate to scaling/constraining
the covariances. But I also take most any opportunity to warn people
not to think too ligthly about PCA :) You can use xpm2ps to combine
the matrices and recolorize according to the range of the combined

Hope it helps,


2009/11/19 Morteza Khabiri <khabiri at greentech.cz>:
> Dear Tsjerk
> Thanks for your help and reply. I thing my question was not clear.
> I want to compare  2 covariance map. but in one map the red colour shows e.g
> 1 nm^2 fluctuation and in other map the red colour shows e.g 0.5 nm^2
> fluctuation. I wanted that both map be in the same scale of colour
> intensity. I mean in both red color max range be 1 nm^2 till the
> comparison of 2 map on a basis of colour intensity be easier. I hope I
> could make my question clear.
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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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