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Re: [lammps-users] Inquiry on special_bonds and first weighting coefficient
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Re: [lammps-users] Inquiry on special_bonds and first weighting coefficient


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 16 Oct 2017 15:26:08 -0400

On Mon, Oct 16, 2017 at 12:37 PM, MASATO KOIZUMI <mkoizumi@...3709...> wrote:
> Dear LAMMPS users,
>
> Hello. I would like for a clarification on special_bonds command. I
> understand that special_bonds only applies to non-bonded interactions, and
> not bonded terms. If this is the case, then I was curious if you could
> inform me the first of the three weighting coefficients as the input
> argument for special_bonds such as
>
> special_bonds 0.0 1.0 1.0
>
> If special_bonds only applies to non-bonded interactions, then I was curious
> if you could inform me the role of the first weighting coefficients which
> determines the weight of the LJ contributions to the 1-2 pairwise
> interactions. Is 1-2 pairwise interaction same as the bonded interaction?

please note, that this is something that you should look up in an MD
text book in the section about force fields. in LAMMPS these are
called "special bonds"; elsewhere these interactions may also be
called "exclusions".

these scaling factors apply to non-bonded interactions, that *also*
are part of the bond topology.
so if two atoms have a bond between them, the first special_bonds
scaling factor applies, i.e. typically both coulomb and lj
contributions are completely excluded (factor = 0.0).
if two atoms are related through two bonds that share one atom (i.e.
typically have an angle potential assigned), but do *not* have a bond
(e.g. the two hydrogen atoms in a water molecule), the 1-3 scaling
term applies. same for dihedrals and 1-4 factors.

axel.

> Thank you.
>
> Sincerely,
>
> Masato Koizumi
>
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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.