[gmx-users] ascii Covariance matrix

Russell Green russellwgreen at gmail.com
Sun Oct 28 06:16:29 CET 2007

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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