[AMBER] PCA variance using Freq = 108.587 * sqrt( 0.6 / Eigenvalue )

From: Muthukumaran R <kumaran.bicpu.edu.in>
Date: Sun, 25 Jan 2015 21:12:40 +0530

Dear Amber users,

I am performing PCA calculations using cpptraj in ambertools 14.
There are 630 C-alpha atoms in my protein and the mass-weighted covariance
matrix is 1890 x 1890.

I extracted the eigenvalues and the first 5 are given below.

1 0.48444
2 0.58309
3 1.08605
4 1.58621
5 1.98272

I want to calculate the percentage of variance for each eigenvector.

According to the suggestions given in the mailing list, I understand that
these are frequencies and should be converted to eigenvalues for
calculating variance.

I tried to convert them using the conversion formula,
Freq = 108.587 * sqrt( 0.6 / Eigenvalue )


But, the first frequency gave a very small eigenvalue (in the range of e-06)

Am I proceeding in the right direction?

I need your valuable suggestions in calculating the percentage variance of
each eigenvector.

Thanks in advance..
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Received on Sun Jan 25 2015 - 08:00:03 PST
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