[gmx-users] Velocity autocorrelation

[Ignacio Fernández Galván]

--- On Sun, 1/4/12, Ignacio Fernández Galván <jellby at yahoo.com> wrote:

> 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?

Silly me, I should have tried the -mol flag for g_velacc from the beginning, how did I miss it? The shape that results is exactly what I was expecting.

However, I'm not completely sure what this flag does. Does it compute the velocity (and its autocorrelation) for the center of mass of each molecule? Does it compute some kind of average per molecule? Something else?

I also tried a workaround: first generate the the centers of mass trajectory with "g_traj -oxt -com", and then try to calculate the corresponding VACF with g_velacc... but g_traj does not write center of mass velocities in the trajectory, hmmm....