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Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
Chemical Reactions in Classical Molecular Dynamics
Jacob R Gissinger1, Benjamin D Jensen2, Kristopher E Wise2
1Materials Science and Engineering Program, University of Colorado, Boulder, CO 80309-0424, USA.
Abstract:
An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics (MD) simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed.
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