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

LAMMPS Framework for Dynamic Bonding and an Application Modeling DNA