How to exclude nonbonded interactions between all atoms of a given phenyl group?

2015-05-28 9:00 GMT+03:00 DengPan <[email protected]>:

Dear everyone:

I have an all-atom polystyrene model(Macromolecules 1996, 29, 4782-4791).
Nonbonded interactions between all atoms of a given phenyl group are
excluded. Does anyone give me some advice? Thanks.

I've had a similar question not long ago
A number of suggestions has been proposed in this thread:
http://sourceforge.net/p/lammps/mailman/message/33848874/

Regards,
Vasily

More specifically, it sounds like you want to exclude pair
interactions between atoms in the same phenyl ring, but not atoms in
different phenyl rings (belonging to different monomers).

First, here's some documentation:

http://lammps.sandia.gov/doc/neigh_modify.html
http://lammps.sandia.gov/doc/group.html
http://lammps.sandia.gov/doc/set.html

Suggestion:

The simplest way to do this would be to use "neigh_modify exclude
GROUP1 GROUP2 molecule". This approach requires you to give different
mol-id numbers to atoms in different monomers. (See below.)

First you have to define a LAMMPS "group" containing all the phenyl
atoms, so your input script file might contain something like this
(assuming 16 atoms in each styrene monomer, and the last 11 atoms in
each monomer belong to the phenyl group)