[gmx-users] combined ED analysis

Berk Hess gmx3 at hotmail.com
Tue Dec 14 15:37:50 CET 2004

>From: "vincenzo venditti" <vincenzovenditti at hotmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] combined ED analysis
>Date: Thu, 09 Dec 2004 17:56:55 +0100
>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?

I don't understand what you want to do.
What do you mean with "fluctuations along eigenvectors"
and with "show different averaged projections"?

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