[gmx-users] g_rmsf over time windows

giordano mancini baloilgiullare at interfree.it
Wed Oct 8 18:56:24 CEST 2008

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.


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