[lammps-users] Questions

Answers below.


Dear Professor Plimpton,

Hello, I am a doctor of Beijing University of Chemical technology in China,
and my research work focuses on studying the relationship between structure
and property of polymers through molecular dynamics simulation with LAMMPS.
In combination with the comments of the reviewer about my manuscript, I have
the following two questions to ask:

(1) According to the lammps manual, the fene keywor sets the 3 coefficients
to 0.0, 1.0, 1.0 for both LJ and Coulombic interactions, which is consistent
with a coarse-grained polymer model with FENE bonds. Thus if the 1-2
coefficient is set to 0.0, then the pairwise interaction is effectively
turned off for all pairs of atoms bonded to each other. However, this is not
consistent with the viewpoint from the literature(Binder K et al, J. Phys.:
Condens. Matter 12 (2000) 6365-6374) that the superposition of the FENE and
LJ potentials leads to a steep effective bond potential with a minimum at
about 0.96σ. How do you think about this?

The LJ term is in the FENE potential itself - see the formula on the bond_style
fene page. So you don't want additional LJ interactions between bonded atoms,
hence you should turn off 1-2 interactions.

(2)For the command of the thermo_style, the attribute "ebond" is referred to
the bond energy, and accrdong to the output values, I think this is the
average value of every bond energy rather than the total value of all bond
energy in the simulated system, is it right?

All output of the thermo command may or may not be scaled by the
number of atoms in the system. This is set by the thermo_modify norm