VMD-L Mailing List

From: Sonibare, Kolawole (kasonibare42_at_students.tntech.edu)
Date: Mon Apr 23 2018 - 13:29:19 CDT

Thank you very much, Prof Bopp.

I intend to calculate self-diffusion coefficients.

Thanks for the resource too.

________________________________
From: Philippe Bopp <philippebopp_at_yahoo.com>
Sent: Monday, April 23, 2018 6:12:21 PM
To: Sonibare, Kolawole
Subject: Re: vmd-l: Calculating Diffusion Coefficient Using VMD

 this is not so easy, see e.g.
 http://ul.qucosa.de/fileadmin/data/qucosa/documents/19515/diff_fund_2%282005%296.pdf

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

 best
-----------------
Philippe A. Bopp
professor of chemistry (retired)

philippebopp AT yahoo.com
-------------
eSSENCE modelling meeting 11-13 June 2018
see https://sites.google.com/site/emultiscale2018/
-------------

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________________________________
From: "Sonibare, Kolawole" <kasonibare42_at_students.tntech.edu>
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
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.