• Outreach

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Apr 23 2018 - 14:01:31 CDT

On Mon, Apr 23, 2018 at 2:29 PM, Sonibare, Kolawole
<kasonibare42_at_students.tntech.edu> wrote:
> Thank you very much, Prof Bopp.
>
>
> I intend to calculate self-diffusion coefficients.

you could do that from within LAMMPS directly. at the time scales
where the einstein relation applies, it doesn't really matter, whether
you record the MSD averaged over all (heavy?) atoms of a molecule or
its center of mass. the error incurred by this simplification will be
smaller than the error on the MSD and thus the self-diffusion
coefficient itself. it might be even more efficient to just pick a
suitable representative atom close to the center of mass and then
define a group of only that atom type.

that said, writing a small script or compiled code to compute a
property like a self-diffusion constant is actually good practice to
do yourself. that way, you can be certain of how it is computed
exactly and don't have to learn how to correctly use somebody else's
code (which can take more effort). most "practical" text books on MD
simulations give examples on how to implement such simple analysis
tools.

since this is so widespread, i would assume, that some smart searching
with google or similar, should lead you to multiple examples, if not
integrated md analysis packages. i recall multiple of them being
advertised here or on the NAMD and LAMMPS mailing lists. so a look at
the corresponding mailing list archives might be helpful as well.

axel.

>
> 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.
>
>
> 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
> -------------
>
> -----------------
>
>
> ________________________________
> 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.
>
>
>

```--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
```