DisARMMD: Distance-Actuated Reaction Mechanisms in Molecular Dynamics

The ability to incorporate heuristic reactions into classical molecular dynamics simulations, in a general way, allows modeling of reactive systems over greatly-increased time scales. DisARMMD, http://www.disarmmd.org, is a protocol that implements complex reaction mechanisms in atomistic, fixed-valence molecular dynamics (MD) simulations. One or more competing, multi-step reactions or series of reactions can be invoked simultaneously, and reaction occurrences are locally relaxed as the simulation progresses. The parallelized algorithm with various added options, including deletion of reaction by-products, reversible reactions, and custom reaction constraints, is available as part of the open-source LAMMPS simulation package as fix bond/react. Large-scale simulations (200,000+ atoms) of the polymerization of polystyrene and nylon 6,6 are presented to demonstrate the current capabilities of DisARMMD. After reaching >99% extent of polymerization, the morphologies of both polymers are analyzed, and the rupture of these highly-entangled systems under uniaxial strain is enabled by defining a chain scission reaction.