Date: Mon, 16 Jan 2012 10:44:20 +0000
Hi,
I'm trying to compute the cosine content of the first PC from the
principal component analysis of a trajectory (10,000 frames). I'm
wondering if AMBER has a tool that helps with this calculation.
I tried using this script to generate an eigen vector of the first PC.
trajin ../alav.bps
matrix covar name covmat out covmat-ca.dat .CA
analyze matrix covmat out evec1-ca.dat vecs 1
However, this script generate only the first eigen vector of the average
structure (instead of all frames)? If I understand the cosine content
formula correctly, I need the first eigen vector of every frame (10,000
frames). Is there a way to print out eigen vectors of every frame? I
tried searching the archive but couldn't find any information about
this. Any advice on how to calculate cosine content of PC would be greatly appreciated.
Thank you very much for your help,
Surasak
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(image/png attachment: cosine-content.png)
