## VMD-L Mailing List

**From:** Sonibare, Kolawole (*kasonibare42_at_students.tntech.edu*)

**Date:** Tue May 01 2018 - 18:22:52 CDT

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Axel, the problem I have is that I have 3 different molecules in my simulation. Therefore, if I use the lammps code, I am not sure of the validity of the result since the molecules are not the same.

Instead, what I did was use the chunk command to output the COM of the different molecules into a dump file and try to use topotools to convert the dump file into a xyz file so that VMD can open it. But right now I'm getting this error.

readvarxyz: read in 0 frames requiring 0 atoms storage.Type map:Max type counts:0

Your comment and that of any other member is appreciated.

________________________________

From: Sonibare, Kolawole

Sent: Tuesday, April 24, 2018 5:34:43 PM

To: Axel Kohlmeyer

Subject: Re: vmd-l: Calculating Diffusion Coefficient Using VMD

Thank you very much for your advice, Axel.

________________________________

From: Axel Kohlmeyer <akohlmey_at_gmail.com>

Sent: Monday, April 23, 2018 8:01:31 PM

To: Sonibare, Kolawole

Cc: Philippe Bopp; vmd-l_at_ks.uiuc.edu

Subject: Re: vmd-l: Calculating Diffusion Coefficient Using VMD

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.
*

*>
*

*> 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/
*

*> -------------
*

*>
*

*> -----------------
*

*>
*

*>
*

*> ________________________________
*

*> 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.

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