[gmx-users] Velocity autocorrelation

[David van der Spoel]

On Apr 4, 2012, at 1:16 PM, Ignacio Fernández Galván <jellby at yahoo.com> wrote:

> --- 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 would guess total velocity of the molecule. I may have implemented this back in the day in the hope that a less noisy graph would lead to better convergence for computing diffusion, but I'm pretty sure that this will give you the same D while losing the vibrational information. Hence the only advantage of this would be speed of execution.
> 
> 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....
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