From: Nakshatra Upadhyay (
Date: Wed Aug 09 2023 - 11:25:19 CDT

Dear all,
I have been trying to calculate the diffusion coefficient of water using
VMD Diffusion Coefficient Tool. However, I got an extremely low diffusion
coefficient value for water (Experimental value ~2.3 m^2/s),
0.0002266 angstrom^2/ns (2.66 m^2/s) was the fit value for diffusion
coefficient. I used a 100ns trajectory having 5000 frames (data saved in
every 10000 steps and time step was 2.0 fs) to calculate the diffusion
coefficient. I used 500 to 2501 frames as lag time and calculated the
diffusion coefficient with a 100-frame interval (Although I got almost the
same values with different lag times). The VMD Diffusion Coefficient Tool
calculated MSD value was almost constant (~720 angstrom^2) for the selected
lag time. Could you please suggest me how to calculate the diffusion
coefficient using VMD?
Sincerely yours,