LAMMPS Framework for Dynamic Bonding and an Application Modeling DNA

TL;DR

This paper extends the LAMMPS simulation software to include dynamic, directional bonds and applies it to model DNA, enabling simulation of chemical reactions and complex molecular interactions.

Contribution

The authors introduce a novel framework in LAMMPS for dynamic bonding, including bond formation, breakage, and conversion, with applications to DNA modeling.

Findings

Successfully modeled DNA dynamics with dynamic bonds

Demonstrated chemical reaction simulation capabilities

Enhanced LAMMPS to support complex bond interactions

Abstract

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.