From: Sonibare, Kolawole (
Date: Mon Apr 23 2018 - 12:22:39 CDT

Thank you very much, Prof Bopp.

I intend to calculate self-diffusion coefficients.

Thanks for the resource too.

On Apr 23, 2018 12:12, Philippe Bopp <> wrote:
 this is not so easy, see e.g.

 you probably need to first define more carefully what (i.e. which diffusion phenomenon)
 you want to study

Philippe A. Bopp
professor of chemistry (retired)

philippebopp AT
eSSENCE modelling meeting 11-13 June 2018


From: "Sonibare, Kolawole" <>
To: "" <>
Sent: Monday, April 23, 2018 6:59 PM
Subject: vmd-l: Calculating Diffusion Coefficient Using VMD

Dear VMD users,

I have a system of heterogenous molecules. I have calculated the Centre of mass coordinates for each molecules using LAMMPS and I have an output file.

I intend to calculate the diffusion coefficient between similar molecules in the mixture. How can I do this please?

Thank you.