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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: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 13 Apr 2018 12:56:42 -0400

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.