On Fri, 2009-10-16 at 11:14 +0800, Yaw Sing TAN wrote:
> Hi,
>
> 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?
The eigenvalue is the variance along the eigenvector. But from he high
value and from your input file it is obvious that you have wrongly
included translations and rotations in your computations. You should
fit your trajectory to a reference structure to get rid of them.
> 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
> go
>
> Thanks for helping!
>
> Yaw Sing
>
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Received on Fri Oct 16 2009 - 07:00:04 PDT
