[gmx-users] combined ED analysis

vincenzo venditti vincenzovenditti at hotmail.com
Thu Dec 9 17:56:55 CET 2004

Dear list,
I want to value the effect of 4 ligands (of various bilogical activities) on 
the dynamic properties of a protein sistem. Then I've performed MD 
simulations (4 ns) of each sistem and I've cheked the sampling for each 
simulation computing the eigenvector overlaps and the cosine contenents.
Then I've concatenated all trajectories together to construct the covariance 
matrix and I've calculated the averaged projections and the rmsf of the 
separate trajectories VS the eigenvector index.
Now, in the light of the recent works of Dr. B. Hess [Phys. Rev. E 62, 8438 
(2000); Phys. Rev. E 65, 031900 (2002)], can I to analyze the differences in 
fluctuations along eigenvectors in which the separate trajectories show 
different averaged projections?

Thanks in advance,

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