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From: <jz7.duke.edu>

Date: Mon, 9 Aug 2004 15:25:10 -0400 (EDT)

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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Received on Mon Aug 09 2004 - 20:53:01 PDT

Date: Mon, 9 Aug 2004 15:25:10 -0400 (EDT)

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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Received on Mon Aug 09 2004 - 20:53:01 PDT

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