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Re: [lammps-users] COM g(r) of Polymer molecular
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Re: [lammps-users] COM g(r) of Polymer molecular


From: Chuanxing Zhan <chuanxingzhan@...16...>
Date: Mon, 16 Apr 2018 01:56:49 +0000 (UTC)

Thanks for your explanation, I'm wondering if you have any example script remained or any helpful information for writing a script. I'm so new in the programming language.
On Friday, 13 April 2018, 6:11:28 PM GMT-5, Shafat Mubin <shafatmubin2@...24...> wrote:


Hi,

For the second method, you can dump the COM of every molecule into an output file, and then write a post-processing script (e.g. in python) to read the COM's every iteration and compute the RDF. I have written a similar python code a few years ago for the COM of a benzene layer.

Shafat

On Fri, Apr 13, 2018, 17:25 Chuanxing Zhan via lammps-users <lammps-users@...44...s.sourceforge.net> wrote:
Thanks for you information! Can you say anything specific about the second method for computing molecular g(r)?  The question is, how to define this COM of molecules to particle and output to trajectory which can use to compute the molecular g(r)? I used the example command to compute the COM of molecule. If i want co continue, what command would be helpful, dump or restart ?
The example command for computing COM of molecule:
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


Thanks,
Kerwin
On Friday, 13 April 2018, 11:56:45 AM GMT-5, Axel Kohlmeyer <akohlmey@...43...4...> wrote:


On Fri, Apr 13, 2018 at 12:40 PM, Chuanxing Zhan via lammps-users
<lammps-users@lists.sourceforge.net> wrote:
> Dear lammps users,
> Hello, everyone! I'm trying to compute the g(r) of COM of polymer, the
> lammps command only compute the g(r) between the atoms. I read previously
> thread in lammps forum, and what they mentioned is I need to build a script
> for calculating COM and defined the molecules. I'm wonder anyone have a
> better way to do the molecular g(r) calculation. Any help would be
> appreciated.

please keep in mind, that a g(r) is a property which computes the
relative probability of point particles in a given system versus the
distribution of an ideal gas.
so any application to molecular systems is of limited meaning.

the easiest approach is usually to pick the atom that is closest to
the center of mass, give it a different atom type number (but the same
force field parameters) and then compute the g(r) for that type of
atom. if you average over a large enough system and long enough
trajectory, the differences to the g(r) of the COM should be
negligible.

a more involved approach would be to compute the COM(s) and output it
to a file and then compute the g(r) in post-processing.

axel.


>
> Thanks !
> Kerwin
>
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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.

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