[DFTB-Plus-User] self-diffusion coefficient

[. Juita]

Dear DFTB+ users,


I am calculating the self-diffusion coefficient from the trajectories obtained from the MD simulation with SCC-DFTB method. However, I get the value 2 orders of magnitude lower compared to the literature value. I checked the space and time unit, unit conversion and it seems that everything is right.  The system is periodic with 10 A box size. In the input file, I specified timestep as 1 fs, MD restart frequency of 100,  and the parameter sets from "3ob" as I have H, N and O in my system. To check the problem, I also carried out simulation of water as the self-diffusion coefficient of water is reported well in the literature, but I still have the same problem.


The issue might be caused by the wrapping or image effect. I tried to modify the coordinate geometry so that all atoms were inside the box (within 10A box size) and re-run the optimisation. The coordinate after convergence, however, shows that some atoms were outside the box, eventhough I have specified the box size in the input file.  May I know how to avoid this wrapping or image effect?


I am wondering if there are any other reasons for the discrepancy in the self-diffusion coefficient. I would appreciate if anyone can assist me with this problem.


Thank you so much for your assistance.

Best regards,

Juita
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