AMBER Archive (2009)

Subject: [AMBER] eigenvalues add up to more than trace of matrix

From: Yaw Sing TAN (
Date: Thu Oct 15 2009 - 22:14:59 CDT


I have a 1725 by 1725 covariance matrix generated by ptraj. According
to the output file which contains the calculated eigenvectors and
eigenvalues, my first eigenvalue of 8571.29110 is higher than 1725.
Does this indicate an error with ptraj or with my simulation? Here is
the ptraj script which I used to generate the evecs.dat file:

trajin prod-1n2e_complete.mdcrd
strip :WAT,Na+
center :1-585
image origin center familiar
matrix covar @CA name cvmat out cvmat.dat
analyze matrix cvmat out evecs.dat name evecs vecs 20
analyze modes fluct out rmsfluct.dat stack evecs beg 1 end 5
analyze modes displ out resdispl.dat stack evecs beg 1 end 5

Thanks for helping!

Yaw Sing

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