Adaptively accelerating reactive molecular dynamics using boxed molecular dynamics in energy space

Abstract

The problem of observing rare events is pervasive among the molecular dynamics community and an array of different types of methods are commonly used to accelerate these long timescale processes. Typically, rare event acceleration methods require an a priori specification of the event to be accelerated. In recent work, we have demonstrated the application of boxed molecular dynamics to energy space, as a way to accelerate rare events in the stochastic chemical master equation. Here we build upon this work and apply the boxed molecular dynamics algorithm to the energy space of a molecule in classical trajectory simulations. Through this new BXD in energy (BXDE) approach we demonstrate that generic rare events (in this case chemical reactions) may be accelerated by multiple orders of magnitude compared to unbiased simulations. Furthermore, we show that the ratios of products formed from the BXDE simulations are similar to those formed in unbiased simulations at the same temperature.

References in corpus (7)

• Escaping free-energy minima
• Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
• A Novel Path Sampling Method for the Calculation of Rate Constants
• Sampling rare switching events in biochemical networks
• Simulating rare events in equilibrium or non-equilibrium stochastic systems
• Action-derived molecular dynamics in the study of rare events
• A simple Boxed Molecular Kinetics approach to accelerate rare events in the stochastic kinetic master equation

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