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

In this article 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 article, we review previous applications of BXD to peptide cyclization, diamond etching, 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 AFM experiments. The latter demonstrate a correlation between the protein’s structural motifs and its potential of mean force (PMF). Simulations of these processes by standard molecular dynamics (MD) is typically not possible, since the experimental timescales are very long. However, BXD yields well-converged and physically meaningful results. Compared to 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.