title: 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.
authors: School of Chemistry, University of Leeds, Leeds LS2 9JT, UK drglowacki@gmail.com.
authors: Jonathan
authors: J
authors: Booth
authors: Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
authors: Saulo
authors: S
authors: Vazquez
authors: Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
authors: Emilio
authors: E
authors: Martinez-Nunez
authors: School of Life Sciences, University of Bradford, Bradford BD7 1DP, UK.
authors: Alison
authors: A
authors: Marks
authors: School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
authors: Jeff
authors: J
authors: Rodgers
authors: School of Chemistry, University of Bristol, Bristol BS8 1TS, UK Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
authors: David R
authors: DR
authors: Glowacki
authors: School of Chemistry, University of Leeds, Leeds LS2 9JT, UK d.shalashilin@leeds.ac.uk.
authors: Dmitrii V
authors: DV
authors: Shalashilin
mesh_terms: D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D001704:Biopolymers
keywords: chemical dynamics; dynamics of proteins; kinetics; molecular dynamics; quantum mechanics