[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)> +

But I'm confused about the "off-diagonal" averages
<(xi-xi_mean)*(zj-zj_mean)>. Do I have to include them
or not and how? 

Thank you in advance for help!


Do you Yahoo!? 
Jazz up your holiday email with celebrity designs. Learn more. 

More information about the gromacs.org_gmx-users mailing list