Diffusion coefficient of free ions

Dear all,

I want to calculate diffusion coefficients of  ions moving in different areas. The diffusion coefficient are affected by the surface, I divided the near surface area into three, wanted to calculate the diffusion coefficient of ions in these three areas, but the ions kept moving from one area to another, so it's difficult to use Forcite->Analysis->MSD to calculate the MSD in one area.

Does anyone have an better idea to get the diffusion coefficient in this case?

Thank you

Jingjing