[gmx-users] essential dynamics analysis
jayant.james at gmail.com
Sun May 31 01:36:57 CEST 2009
I have a 7ns MD run of a protein and the RMSD of the protein had stabilized
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
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?
Jayasundar Jayant James
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users