From: Josh Vermaas (
Date: Thu Jan 30 2014 - 08:12:14 CST

Hi Juita,

Are diffusion constants usually reported from QM studies? In my
experience, short simulations (<1ns) tend to be in the regime where
things are settling down and the Einstein relation gives nonsensical
answers (atoms haven't had the time to change directions enough for it
to be a good random walker yet). Some other possible explanations:

-Trajectory spit out by DFTB may not be in the units you or VMD expect
(No idea if this is true, but just looking at the docs quickly, DFTB
uses Bohr instead of Angstrom internally, so make sure you check the
units for both space and time!).
-Is this a periodic system? If so, have you checked wrapping? There
should be no wrapping.

Your shortcut should in principle work, but it never hurts to check an
alternative formulation for determining diffusion, and keep in mind that
computational diffusion constants do not perfectly agree with literature
values in general (although 2 orders of magnitude is a bit extreme).

Good luck!
-Josh Vermaas

On 01/30/2014 03:21 AM, . Juita wrote:
> 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