[gmx-users] How to compute covariance???

Semen Esilevsky yesint4 at yahoo.com
Tue Jan 4 10:43:51 CET 2005

 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
 (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)> +
 But I'm confused about the "off-diagonal" averages
 <(xi-xi_mean)*(zj-zj_mean)>. Do I have to include
 or not and how? 
 Thank you in advance for help!

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