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: Fri, 23 Jul 2010 17:43:57 +0000

> I open the IED and found 20 eigenvectors, the 1st eigenvectors has a middle value of 20
> (the value where the cursor stay when i click the eigenvector's box, but I can move the
> cusors from -20 to 30.

These are the minimum and maximum values from the projection of the 1st eigenvector on the trajectory.

> How can I know if the first 3 vectors represent over 90% of the movement in the protein?

You would have to compare the sum of the first 3 eigenvalues to the sum of all eigenvalues. The eigenvalues are essentially variances.
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Received on Fri Jul 23 2010 - 11:00:05 PDT
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