[gmx-users] Velocity autocorrelation

[Ignacio Fernández Galván]

--- On Fri, 30/3/12, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> No need, I think it is just fine!
> What your seeing is the average vacf per atom, and
> apparently there are 
> correlations between the vibrations which cause the
> oscillation. In 
> theory both VACF should be the same but they are relatively
> close. A 
> longer simulation is always good of course.

But how can I extract a meaningful relaxation time from there?

Maybe instead of individual atoms, I should analyze the VACF of the center of mass of each molecule, and the rotational ACF. The latter I know how to do it. Is there an "easy" way to calculate the former?

Anyway, in this case it makes sense to divide the system in molecules, because that's what it is, but if it were say a protein, what would be the best way to analize the VACF and get some meaningful relaxation time?

Thank you,
Ignacio