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 structures? 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? -- Pawan
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