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Re: [lammps-users] Opening Centre of Mass (COM) dump file in VMD
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Re: [lammps-users] Opening Centre of Mass (COM) dump file in VMD


From: "Sonibare, Kolawole" <kasonibare42@...6053...>
Date: Fri, 20 Apr 2018 02:01:52 +0000

Thank you for your response earlier, I have requested for subscription to the VMD mailing list.


I have a question concerning the dump file used by these blocks of codes:


compute cc1 all chunk/atom molecule ids once

compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector


compute mychunk all chunk/atom molecule ids once
compute msd all msd/chunk mychunk
fix 2 all ave/time 1000 1 1000 c_msd[*] mode vector file msd.data


I have a heterogeneous mixture of molecules and want to calculate the diffusion coefficient and RDF for molecules of the same type. Now, it seems from what I have read here that LAMMPS can't identify what molecules belongs to what component (that is, LAMMPS can't tell if it is a benzene or naphthalene molecule). Or maybe I'm wrong.


Can you please point me in the right direction to do this calculation? Thank you very much.




From: Axel Kohlmeyer <akohlmey@...24...>
Sent: Monday, April 16, 2018 10:47:01 PM
To: Sonibare, Kolawole
Cc: lammps-users@lists.sourceforge.net
Subject: Re: [lammps-users] Opening Centre of Mass (COM) dump file in VMD
 
On Mon, Apr 16, 2018 at 5:30 PM, Sonibare, Kolawole
<kasonibare42@...6053...> wrote:
> Dear Lammps User,
>
>
> I have just written out the Centre-of Mass (COM) coordinates for the
> molecules in my simulation using:
>
>
> compute cc1 all chunk/atom molecule
> compute myChunk all com/chunk cc1
> fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
>
>
> The intention is to use this to get the radial distribution function, g(r)
> on VMD as I have read here. The problem I have is that VMD cannot directly
> open this file. Please how can I get this done? Thank you very much.

this is not a LAMMPS question, but a VMD question. you should post
these kind of questions on the VMD mailing list.
the *very* obvious answer is: write a little tool, that converts the
output you have into a file format that *is* by VMD.
for details on that, you *definitely* should read the VMD docs and ask
further questions on the VMD mailing list.

axel.

>
>
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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.