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<DIV></DIV>>From: "Berk Hess" <gmx3@hotmail.com>
<DIV></DIV>>Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
<DIV></DIV>>To: gmx-users@gromacs.org
<DIV></DIV>>Subject: RE: [gmx-users] combined ED analysis
<DIV></DIV>>Date: Tue, 14 Dec 2004 15:37:50 +0100
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>>>From: "vincenzo venditti" <vincenzovenditti@hotmail.com>
<DIV></DIV>>>Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
<DIV></DIV>>>To: gmx-users@gromacs.org
<DIV></DIV>>>Subject: [gmx-users] combined ED analysis
<DIV></DIV>>>Date: Thu, 09 Dec 2004 17:56:55 +0100
<DIV></DIV>>>
<DIV></DIV>>>Dear list,
<DIV></DIV>>>I want to value the effect of 4 ligands (of various bilogical
<DIV></DIV>>>activities) on the dynamic properties of a protein sistem. Then
<DIV></DIV>>>I've performed MD simulations (4 ns) of each sistem and I've cheked
<DIV></DIV>>>the sampling for each simulation computing the eigenvector overlaps
<DIV></DIV>>>and the cosine contenents.
<DIV></DIV>>>Then I've concatenated all trajectories together to construct the
<DIV></DIV>>>covariance matrix and I've calculated the averaged projections and
<DIV></DIV>>>the rmsf of the separate trajectories VS the eigenvector index.
<DIV></DIV>>>Now, in the light of the recent works of Dr. B. Hess [Phys. Rev. E
<DIV></DIV>>>62, 8438 (2000); Phys. Rev. E 65, 031900 (2002)], can I to analyze
<DIV></DIV>>>the differences in fluctuations along eigenvectors in which the
<DIV></DIV>>>separate trajectories show different averaged projections?
<DIV></DIV>>
<DIV></DIV>>I don't understand what you want to do.
<DIV></DIV>>What do you mean with "fluctuations along eigenvectors"
<DIV></DIV>>and with "show different averaged projections"?
<DIV></DIV>
<P>> </P>
<P>If I've for example for the 4 sistems under analysis differnt averaged projection along the second eigenvector:</P>
<P> sistem 1 sistem 2 sistem 3 sistem 4</P>
<P>vector 2 3.378 2.547 -3.375 -2.540</P>
<P>And I've for the same sistems along the same eigenvector different rmsf value:</P>
<P> sistem 1 sistem 2 sistem 3 sistem 4</P>
<P>vector 2 1.2 0.8 0.5 0.3</P>
<P>Could I say that sistem 1 is more flexible than the other sistem along this direction of motion?</P>
<P>Best regards,</P>
<P>Vincenzo</P>
<P> </P>
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