rs@md: Introducing Reactive Steps at the Molecular Dynamics Simulation Level
Myra Biedermann, Diddo Diddens, Andreas Heuer
Abstract
A concept is presented to extend molecular dynamics simulations by the so-called reactive steps, during which transitions from reactant to product molecules are performed with physically correct transition probabilities. This goes along with an instant exchange of the employed force field. We provide a detailed mathematical derivation for how the acceptance probability for such reactive steps can be computed from molecular reaction rates and introduce a simulation program that performs such reactive step molecular dynamics simulations. Our program is designed in a modular fashion and can thus be extended to any conventional molecular dynamics program. Furthermore, the working principle of these reaction rate-based reactive step simulations is demonstrated by applying them to a reactive model system based on associating and dissociating Lennard-Jones particles and compared to a similar approach from Nagaoka et al. which uses the Metropolis Monte Carlo scheme for the reactive steps. Overall, we find that our approach not only recovers the correct thermodynamics but also ensures proper kinetics, that is, the correct time evolution of the system.