[gmx-users] How to compute covariance?
Semen Esilevsky
yesint4 at yahoo.com
Tue Dec 28 09:28:14 CET 2004
Dear gmx users,
I'm sorry for stupid question, but I can't find the
answer for two days :(
The problem is how to compute the correlation (or
covariance) of two particular atoms using the
MDtrajectory. I just need a correct equation for this
(not the program, which does this).
If I have the atoms i and j I'd rather compute the
covariance between them as
cov_ij = <(xi-xi_mean)*(xj-xj_mean)> +
<(yi-yi_mean)*(yj-yj_mean)> +
<(zi-zi_mean)*(zj-zj_mean)>
But I'm confused about the "off-diagonal" averages
like
<(xi-xi_mean)*(zj-zj_mean)>. Do I have to include them
or not and how?
Thank you in advance for help!
Semen
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