Hello All,
I have a protein with 618 residues and I used ptraj to perform PC analysis
on the protein.
This code:
*rms first out rms .CA,C,N*
*image center*
*
*
*matrix mwcovar name mixedma .CA,C,N*
*analyze matrix mixedma out evecs.dat.mixed vecs 5*
gave me a 5562x5562 matrix file which also has these lines:
5562 5562
1 0.80680
2 1.09819
3 1.67464
4 2.01560
5 2.39907
Do the last 5 lines correspond to the 5 eigenvectors? If yes then the
contribution of
1st eigen vector in explaining the motion = 0.8068/[0.8068+1.098+...2.399]
But this would mean that contribution of 2nd eigenvector is more than 1st
eigenvector which seems incorrect since
1>2>3>4>5.
Can someone explain what I am missing here?
Thanks
P
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Received on Thu Jul 25 2013 - 13:30:03 PDT
