Hello,
I am just trying to make sure that I understand the special_bonds command in lammps. I am using a FENE bond to simulate different polymer topologies. The FENE bond already has a lennard jones potential built into it, but I am also using the lj/cut command for atoms that are not bonded together. I am just trying to make sure that for atoms that are bonded together, I am not calculating the lennard jones potential twice, one by using lj/cut, and one by using the FENE bond. Having read the special_bonds page, it seems to me that if I use special_bonds fene dihedral no, I will not be calculating the lj potential twice, because it turns off pair style interactions for bonded atoms. Is what I am saying true? I have already read the special_bonds page; I am just double checking.
Thank you