Hi Tsjerk
Whether that's enough is largely dependent on the size of your protein
You should check whether you went beyond relaxation by inspecting the
cosine content of the first few eigenvectors.
This by itself does not mean anything. If it levels off at 0.1 nm,
okay, that's pretty good, but the further you go, the more
possibilities you have for getting a certain RMSD. It's a distance
measure. Being at 10 cm distance from you will make it easy to
localize me, but if I'm at 10 miles, you wouldn't now where to search.
I could well go 10 miles and then start following a circle, and you'd
argue, based on the distance, that I'd stopped moving!
Ok; i have not checked it still; I wanted to check deviation and
fluctuations first to see if some unexpected/abnormal behavior
in the protein. but now I got your point about rmsd and relaxation
That is indeed the case. And if your system had converged, there
wouldn't be a difference between the average structures from
subtrajectories A and B. The RMSF is only defined about the mean
structure. You don't want to go into non-central moments. If you have
the average structure for the whole trajectory, you can use it as the
reference to calculate the RMSF. I believe that g_rmsf has an option
to use deviations from the reference rather than from the calculated
average structure.
Actually the manual says it (option -od?). My fault. Anyway it has been
useful to think about it.
Hope it helps,
It did; thank you.
cheeres
giordano
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