t.a.wassenaar at chem.rug.nl
Fri Aug 27 12:31:38 CEST 2004
This depends a bit on what you want to see. If you project the
trajectory of part of the protein on the eigenvectors of the whole
protein, you will see how this part participates in the collective
motions of the whole thing, whereas constructing the covariance matrix
on part of the protein and diagonalizing that, will only reveal
collective motions of that part without showing how these are connected
to the rest of the protein.
Ruben M Buey wrote:
> Hi all,
> I´m trying to perform a combined essential dynamics analysis of
> different CONCOORD simulations of a very big system (more than 40000
> I think it would be better to do a combined-ED analysis on separately
> parts of this big system.
> Should I construct the covariance matrix with the whole system C-alpha
> and then project onto the corresponding eigenvectors only the part of
> the trajectory I am interested in? Or should I construct the
> covariance matrix only for the small set of atoms I am interested in?
> Thanks a lot for your kind attention,
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