[gmx-users] essential dynamics

pawan raghav pwnrghv at gmail.com
Tue Aug 17 09:56:01 CEST 2010

Hi all,

I have a confusion regarding "Essential Dynamics". I have read so many
papers regarding PCA and ED most of the papers among them explained
eigenvectors and eigenvalues are as follows:

if a protein has 207 C alpha residues then the total no of eigenvectors are
3N X 3N, where N= no. of atoms i.e. 3 X 207 = 621 eigenvectors. is it means
that an eigenvector represents an C-alpha residue?

But manual described that representations the direction of motions.

But 3N X 3N is a covariance matrix that means this represents 621 X 621
eigenvectors is it true?

Then when we plot a 2dproj.xvg file between eigenvector 1 and eigenvector 2,
is it mean to plot a 2d graph between first two C-alpha atoms or first two

Please clearify me where I was wrong.

The 2d graph shows oval and random large trajectory graph which represents
the independent and dependent motion, may I know what does it mean?

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