[gmx-users] Eessential dynamics analysis

sunita at chem.iitb.ac.in sunita at chem.iitb.ac.in
Thu Jan 11 06:10:59 CET 2007

Dear friends,

I performed essential dynamics (ED) analysis on my peptide using g_covar
and g_anaeig. The first two eigenvectors represent 58% of the total
positional fluctuation. The projection of the trajectory on eigenvectors
gives me the proj.xvg file. From which I extracted the projection along
the first and second eigenvectors.I plotted the histgram separately for
the projection along the first and second eigenvectors to see their

I observed the range of distribution along first eigenvector is less than
the second eigenvector. But in principle the range of first eigenvector
should be greater than second (ref: Proteins, 1993, 17, 412-425) since
first eigenvector has highest eigenvalue means higher mean square
displacement so the spread of distibution should also be more. In contrast
I am getting greater spread for second eigenvector.

Could you please comment why I am getting so...?


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