[gmx-users] Concoord-ED

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Fri Aug 27 12:31:38 CEST 2004

Hi Ruben,

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 
> atoms).
> 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,
> Bests,
> Ruben

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