[gmx-users] combined ED analysis
vincenzovenditti at hotmail.com
Thu Dec 9 17:56:55 CET 2004
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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