[gmx-users] sampling techniques when calculating diffusion coefficients using Green-Kubo

Ying Chen yc7571 at vt.edu
Thu Feb 5 22:10:55 CET 2015

Dear all,

I am trying to use Green-Kubo method to estimate diffusion coefficients.
For a simple box of pure water, MSD gives D~2.7E-9 m2/s, but velocity
autocorrelation function (VACF) method gives D~6.8E-9 m2/s, and this value
becomes smaller with smaller timestep dt, but it still doesn't reach ~3E-9
for dt~0.00002 ps and total time=2 ps.  I saw this page
mentioned that VACF may decay very slowly and this method becomes very
costly, "it is often desirable to use more sophisticated sampling
techniques when estimating transport coefficients using Green-Kubo-type
analyses". Does anyone know what these techniques are or where we can find
them? Thanks a lot!


More information about the gromacs.org_gmx-users mailing list