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: Sat, 24 Jul 2010 08:26:27 +0100

> 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%.

No, you misunderstood. The values above are some arbitrary (possible just
interpolated) values from the projections that you have obtained from ptraj's
'projection' command. What you want is the eigenvalues from the file which you write
with the 'analyze matrix out' command. For the sum you will have to either compute all eigenvectors/eigenvalues or directly analyze the matrix (sum of the diagonal elements)
which you can write with the 'matrix' command.


Dr. Hannes Loeffler           email:
STFC Daresbury Laboratory,    tel:   +44-1925-603367
Warrington,                   fax:   +44-1925-603634
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Received on Sat Jul 24 2010 - 00:30:03 PDT
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