[lammps-users] Some questions about FENE potential

Dear lammps users and the author of lammps,
FENE potential in lammps includes two terms: the first term is the
attractive, the 2nd Lennard-Jones term is repulsive. The first term
extends to R0, the maximum extent of the bond. The 2nd term is
cutoff at 2^(1/6) sigma.

When modelling polymer system, I define FENE bond style, and provide the
coefficients of the style, and also use command “special_bonds 0.0 1.0 1.0”.
So for the bonded atoms the lj potential is calculated in lammps FENE
potential, which may be efficient, but I have a question: for the bonded monomers, lj
potential is cut at 2^(1/6) sigma, which is not always the general case in polymer
simulation. For example, if I want to cut lj potential between all monomers at
2.5 sigma, how should I do? There is a method, but I am not sure: only the
first attractive term in present FENE potential is needed, and then calculate lj
potential between all monomers via “special_bonds 1.0 1.0 1.0”. Is that right?


Zhimin Xiong

The typical way to do what you are asking is define a FENE
bond between bonded atoms and a separate pair potential
between all monomers. The cutoff for the FENE part is
always short, but the cutoff for the pair potential can be
whatever you want (e.g. 2.5). Setting special_bond 0 1 1
simply sets FENE to be the only potential computed
between bonded atoms, which is what you want. The long
cutoff will be used between all other pairs.

Note that the short-cutoff LJ that is computed with FENE is
not a pair potential - it is really part of the FENE bond itself
to provide a repulsive core.