Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER?

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Date: Sun, 25 Jul 2010 10:10:18 +0000

> Is the 790. and 71. are eigenvalue of the first two eigenvectors?


> I guess to calculate the percentage for the first three eigenvalues,
> i should add the number of the ****1 (i.e. 790.12599) and ****2.
> (ie. 71.09028) number and over all the sum of the rest's eignevalues.
> am I correct?

Yes. Just make sure to use ALL modes and to set the 'vecs' option of the
'analyze matrix' command accordingly.

What wonders me, however, is that the matrix from your example is
1563x1563 = 521 atoms while in the original mask you have chosen 720.
Scanned by iCritical.
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Received on Sun Jul 25 2010 - 03:30:03 PDT
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