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Re: [lammps-users] lj/cut and harmonic bond
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Re: [lammps-users] lj/cut and harmonic bond


From: Steve Plimpton <sjplimp@...24...>
Date: Wed, 10 Dec 2014 06:03:53 -0700

The special_bonds command Axel indicated allows you
to turn on/off/scale LJ (or pair) interactions between atoms
bonded to each other.  For 2 atoms connected by a harmonic
bond, you can have bond + alpha*LJ, where alpha is any scale
factor from 0.0 to 1.0.  The default is 0.0.

Steve

On Wed, Dec 10, 2014 at 4:41 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Wed, Dec 10, 2014 at 5:47 AM, Saikat Basu <sspsb2@...33....2311...> wrote:
>
>  Hi all,
>
>  In my system I have 2 particles connected by harmonic bond. And for
>  this interaction I have specified a bond coefficient.
>  Now, I wish to apply a LJ interaction, via lj/cut command,
>  on top of harmonic interaction. Will it  work then ?

this is a *very* unusual model. typically, when you have explicit
bonded interactions, non-bonded interactions between the atoms that
are bonded are ignored. this is called 1-2 exclusions and only
computed between periodic images (if they are within the cutoff). same
goes for 1-3 and 1-4 neighbors for angles and dihedrals. the scaling
factors for this are controlled with the special_bonds command.

please update your basic force field knowledge by re-reading the
corresponding chapters in your favorite text book on MD and their
force fields before continuing.

axel.

>
>  I am doing this. Somehow it is not working.
>  In a short, there dynamics is governed by the harmonic interaction only.
>  LJ interaction is not taking count.
>  Can you please give me any idea to over come it.
>
>
>
> Best,
> ******************
> Saikat Basu
> Senior Research Fellow
> Room no:C/312,Centenary Building
> Department of Solid State Physics
> Indian Association for the Cultivation of Science,
> Jadavpur
> Kolkata-700032
> Ph no- 03324734971(extn- 2114)
>
>
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--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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