Hello folks,
I am following the tutorial by Cheatham et al at AMBER15 work shop at
London to perform PCA of a structure in MD simulation.
http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/
I extracted the eigenmode data file from the covariance matrix of
coordinates followed by the projection of the structure along the few
principle components (PC) using the "projection" command as described in
the in above tutorial. If I understand it correctly, it is the dot product
of the eigen vector and the coordinates of this frame in Angstrom. Please
correct me if it is not true. What does it means that the coordinates
"match well" with the PC. What the relatively high projection to one
particular mode reflects, some description would be really helpful.
My other question is how do I know how much does the corresponding PC
contribute to the total motion.
Thank you in advance.
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Received on Sat Jun 04 2016 - 06:30:02 PDT
