Dear hannes,
thank you very much for your help. Your information is very useful. I would like to reconfirm if I have understand this correctly.
In my suitation, I have 20 eigenvalues, when I open the PCA data with IED in VMD. I found the cursors originally stop at the following values (20, 10, 5, 3, -1, -2, -3, -5...) do you mean I should sum up all these 20 values and divide by 35 (i.e. the first three eigenvalue (20+10+5), to see if the value larger than 90%.
best regards,
Catherine
> From: hannes.loeffler.stfc.ac.uk
> To: amber.ambermd.org
> Date: Fri, 23 Jul 2010 17:43:57 +0000
> Subject: Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER?
>
> > 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.
> --
> Scanned by iCritical.
>
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Received on Fri Jul 23 2010 - 21:00:03 PDT
