On Apr 4, 2012, at 1:16 PM, Ignacio Fernández Galván <[email protected]> wrote:
> --- On Sun, 1/4/12, Ignacio Fernández Galván <[email protected]> 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.... > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
