[gmx-users] ascii Covariance matrix

Arneh Babakhani ababakha at mccammon.ucsd.edu
Sun Oct 28 07:16:37 CET 2007

Hi Russell,

Check out the discussion here:



> Hello all,
>     I'm trying to handle covariance data using the ascii output from
> g_covar. I let g_covar calculate a covariance matrix for 198 alpha carbons
> of a protein, which should give me a 594 x 594 matrix. This is probably a
> simple issue, but I'm confused by the ordering of the elements in the
> ascii
> file. It contains a matrix arranged as 117612 x 3. So, how does this
> translate into a 594 x 594 matrix? Also, I know there's an option in
> g_covar
> to output an xpm file that averages values to create a matrix where each
> row
> and column correspond to one atom, but I'm unclear how this is done. I
> would
> like to do this using the data from the ascii file. If anyone could
> explain
> this to me, or tell me were to look, I would really appreciate it.
> Thanks in advance,
> Russell Green
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Arneh Babakhani
McCammon Lab
Department of Chemistry & Biochemistry
University of California at San Diego
9500 Gilmand Dr MC 0365
La Jolla, CA 92093-0365
(858)534-4974 (FAX)
ababakha at mccammon.ucsd.edu

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