[gmx-users] How much data to choose eg for an rmsd matrix

[K.A. Feenstra]

Marc Baaden wrote:
[...]
> thanks for the reference, David. Looks very interesting, although I
> don't have 800 microseconds of data (*envy*). It is certainly an
> analysis idea that I will keep up.
> 
> But considering my original question, I really want the standard/simple
> RMSD matrix, and only wondered how coarse I should/could get.

It really depends on the properties you are going to look at. Generally
speeking, any time scale could be relevant so there is no rule of thumb
there, I'm afraid. The 'coarse-graining' series you propose seems like
a reasonable thing to do, but you could better do it the other way around.
First take e.g. 100 frames over your whole trajectory (i.e. one every
100 ps for a 10 ns traj). Then take e.g. 200 or 500 frames and see if
there are any interesting new features. If you have some specific points
where (interesting) transitions occur, you can always make a more detailed
matrix for only that part of the traj. E.g. if there is a transition around
2.5 ns, you could make a separate matrix from 2400 to 2600 ps taking one
frame each 1 ps.
(Hmm, I thought this would be a short-version answer... ;-)


-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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