## VMD-L Mailing List

**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Tue May 01 2018 - 19:25:54 CDT

**Next message:**Philippe Bopp: "Re: Calculating Diffusion Coefficient Using VMD"**Previous message:**Sonibare, Kolawole: "Re: Calculating Diffusion Coefficient Using VMD"**In reply to:**Sonibare, Kolawole: "Re: Calculating Diffusion Coefficient Using VMD"**Next in thread:**Philippe Bopp: "Re: Calculating Diffusion Coefficient Using VMD"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Tue, May 1, 2018 at 7:22 PM, Sonibare, Kolawole

<kasonibare42_at_students.tntech.edu> wrote:

*> 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.
*

you are not making any sense to me. you attempt something complex with

questionable advantages, where you obviously have no experience in

doing it, and not the skill to figure it out on your own.

while on the other hand what i am suggesting is straightforward to do

after carefully reviewing the provided documentation and examples. you

can easily separate different molecules into groups and do the

computations separately for groups.

using .xyz format files makes no sense, either, since that file format

does not include the box information and thus you cannot easily take

box crossings into account. the msd compute in LAMMPS does that

automatically as well.

axel.

*>
*

*> ________________________________
*

*> 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.
*

-- 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.

**Next message:**Philippe Bopp: "Re: Calculating Diffusion Coefficient Using VMD"**Previous message:**Sonibare, Kolawole: "Re: Calculating Diffusion Coefficient Using VMD"**In reply to:**Sonibare, Kolawole: "Re: Calculating Diffusion Coefficient Using VMD"**Next in thread:**Philippe Bopp: "Re: Calculating Diffusion Coefficient Using VMD"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]