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Re: [lammps-users] Angle criteria to add bound between two atoms
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Re: [lammps-users] Angle criteria to add bound between two atoms


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 7 May 2018 10:32:58 -0400

On Mon, May 7, 2018 at 6:03 AM, abbas abouei via lammps-users
<lammps-users@lists.sourceforge.net> wrote:
> Dear lammps users,
> I would like to apply the bound between two water molecules with two
> criteria at the same time, one the distance between two oxygen atoms and
> secone the angle of O-H.....O in Lammps. The distance criteria can be added
> by fix bond/create command but I dont have any idea about how I can add the
> angle criteria. do  you have any recommendation?

tinkering with the bonding topology is best done outside of LAMMPS.
complex operations will require some programming, so that would be
easier to do with some suitable scripting language. reading/parsing of
LAMMPS topology data can be done with different tools. for example,
there is Pizza.py, which is python based, and there is VMD, which uses
Tcl scripting.

what you want to do is very uncommon (and in conflict with chemistry,
too). also, i am wondering whether you have considered the implication
of adding this bond in terms of exclusion of non-bonded interactions.
how many of these special bonds do you need to create and what is
their overall purpose? if my crystal ball is correct, adding them to
the topology may not be producing the effect you are looking for.

axel.



> Bests,
> Abbas
>
> A.Abouei Mehriz
>
>
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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.