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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