[gmx-users] Velocity autocorrelation

[Ignacio Fernández Galván]

--- On Sun, 1/4/12, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> It depends what you want to compare to.

Fair enough. For the moment I don't want to compare to anything. I just want to extract a number of uncorrelated configurations from the simulation, and to know what's the minimum interval at which I should sample configurations.

Something like what's explained in pp. 164-ff of this book:
http://books.google.es/books?id=GT9oPnAEkEQC

> The relaxation time of a
> velocity averaged per atom can be analyze by fitting the vac
> to y = exp(-t/tau). This gives 5 fs in your graph.

5 fs? Don't you mean 5 ps? In that case, how do arrive to such value? It can't be a simple exponential fit, because the function is oscillating. Do you just guess it by the way the amplitude shrinks?

This is my main problem, I don't see how one can fit an exponential to an oscillating function.

Thank you,
Ignacio