[gmx-users] essential dynamics analysis

[jayant james]

Hi!

I have a 7ns MD run of a protein and the RMSD of the protein had stabilized
after 3ns.

I am about to performed essential dynamics (ED) analysis (using the commands
g_covar and g_anaeig) on the trajectory and I have a few
questions/clarifications.

1) Should ED analysis be performed only on the segment of trajectory wherein
the protein's RMSD has equilibrated, am I right?  Because I have the notion
that harmonic analysis of a trajectory can only be performed when the
protein is undergoing fluctuations about a minimum. In other words once rmsd
stabilizes, then one can perform a harmonic analysis.

2) Which would be a better marker to see if the protein has equilibrated to
the simulation environment the RMSD of the protein or the projection of
motion along Eigen vectors?

3) When I plot the root mean square fluctuation (r.m.s.f.) of the amino
acids am I plotting the motions (of c-alphas) orthogonal to the principal
component, Eigen vector 1? and would I wrong in saying that these regions of
the protein which have large fluctuations, (say greater than 2 angstroms),
do experience anharmonic fluctuation?

If so how can I pick up anharmonic fluctuations?

Thank you

JJ






-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
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