Diffusion Constant

Using a GROMACS trajectory you can calculate diffusion constants both with Einstein (g_msd) and Green-Kubo (g_velacc and then g_analyze) equations. While g_msd is self-explanatory, using g_velacc starting from the version 4.0 is a bit trickier.

To calculate the diffusion constant of the particle via Green-Kubo equation the following commands should be supplied:

g_velacc -acflen 1001 -nonormalize -mol -n atoms.ndx -s topol.tpr

where 'atoms.ndx' should contain the numbers of the atoms which form the particle of interest. By default, you will obtain 'vac.xvg' with a linear velocity autocorrelation function (VACF).

Then to obtain the diffusion constant type:

g_analyze -f vac.xvg -integrate

This will give an integral of the VACF in [nm²/ps].

Finally, if you've obtained the solution for the integral value of 6 x 10^-5 nm²/ps from VACF, multiplying this quantity by 10^-6 (to simultaneously convert nm² to m² and ps to s) and dividing it by 3 (according to Green-Kubo equation) would yield 2 x 10^-11 m²/s. This is the value of diffusion constant.