Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

Abstract

In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.

Enhancing Automated Reaction Discovery with Boxed Molecular Dynamics in Energy Space

“…For this reason, we present in this paper a new combined methodology where the high‐energy MD simulation algorithm of AutoMeKin is substituted by a rare event acceleration technique recently developed by two of the authors . The accelerated method is called Boxed Molecular Dynamics in Energy space (BXDE) and is based on their previous BXD method . BXDE scans through potential energy “boxes”, accelerating the observation of reactive events by many orders of magnitude …”

“…[72] The accelerated method is called Boxed Molecular Dynamics in Energy space (BXDE) and is based on their previous BXD method. [73][74][75][76] BXDE scans through potential energy "boxes", accelerating the observation of reactive events by many orders of magnitude. [72] To test the combined AutoMekin-BXDE methodology we have chosen the ozonolysis of α-pinene.…”

An automated method to find transition states using chemical dynamics simulations

“…Several accelerated dynamics (AD) methods have been proposed in the literature to simulate infrequent events, and some of them have been implemented in popular molecular dynamics programs. Our method and the AD methods share in common the use of high‐energy or high‐temperature dynamics.…”

A Blind Test of Computational Technique for Predicting the Likelihood of Peptide Sequences to Cyclize

“…3−5,24,25 We have used boxed molecular dynamics (BXD), a method that overcomes the long time scale and high free energy problem. Previously BXD has been successfully employed to simulate a wide range of difficult processes such as protein unfolding in atomic force microscopy experiments, nonenzymatic peptide cyclization, and diffusion.…”