AMBER Archive (2004)Subject: AMBER: question about covariance matrix from ptraj
From: jz7_at_duke.edu
Date: Mon Aug 09 2004  14:25:10 CDT
Dear all,
I have two questions about the covariance matrix from ptraj. Hope I can
get some help from the amber group.
First if the number of atoms is N. Then the covariance matrix is 3N by 3N
(each atom has three cordinates). But I am wondering what format is the
matrix. Are the three cordinates for one atom next to each other(atom1(x,y,z),
atom2(x,y,z), ...)? Or is the correlation along each axis grouped
together (like atom1(x), atom2(x),...atom1(y), atom2(y)...)?
Second it is not easy to study the relationship between each atom in this
3N by 3N matrix. So I am wondering if there is a way that I can reduce
the matrix to N by N (it means each element represents the correlation
between atom i and atom j; combine the seperated information along three
axes together)?
Thanks a lot!
Sincerely,
Jeny

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