This is a fork of the lammps molecular dynamics code which I modified to my needs.
I use lammps to simulate a coarse grained DNA model.
The major modifications lie in 3 files
This is a harmonic-cosine breakable bond
This is a dihedral that scales with the middle bond.
In my dna model this dihedral connects complimentary strands, it dies down as inter-strand bonds are broken.
This is a very simple pairwise interaction, it is mainly there to avoid bond crossing.
It is simply the repulsive half of the harmonic potential.