VMD-L Mailing List

From: . Juita (juita_at_uon.edu.au)
Date: Thu Jan 30 2014 - 03:21:45 CST

Dear VMD users,

I am doing calculation of self-diffusion coefficient from the trajectories data obtained from DFTB+ simulation. I am wondering whether I do the correct calculation. I utilise VMD to calculate and plot the RMSD, then squared it to get the plot of MSD (mean square displacement). The self-diffusion coefficient is estimated from the slope of MSD vs time plot using Einstein relation. However, I get the value 100 times less compared to the literature value. I would appreciate any assistance for this problem.

Thank you so much for your assistance.
Best regards,
Juita