  We have extended the Large-scale Atomic/Molecular Massively Parallel
Simulator (LAMMPS) to support directional bonds and dynamic bonding. The
framework supports stochastic formation of new bonds, breakage of existing
bonds, and conversion between bond types. Bond formation can be controlled to
limit the maximal functionality of a bead with respect to various bond types.
Concomitant with the bond dynamics, angular and dihedral interactions are
dynamically introduced between newly connected triplets and quartets of beads,
where the interaction type is determined from the local pattern of bead and
bond types. When breaking bonds, all angular and dihedral interactions
involving broken bonds are removed. The framework allows chemical reactions to
be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The
resulting DNA dynamics illustrate the power of the present framework.
