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

Jonathan Booth, Saulo Vazquez, Emilio Martinez-Nunez, Alison Marks, Jeff Rodgers, David R. Glowacki, Dmitrii V. Shalashilin*

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

16 Citations (Scopus)
301 Downloads (Pure)

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 othermethods of acceleratedMD

Original languageEnglish
Article number20130384
Pages (from-to)1-13
Number of pages13
JournalPhilosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
Volume372
Issue number2021
DOIs
Publication statusPublished - 6 Aug 2014

Keywords

  • Chemical dynamics
  • Dynamics of proteins
  • Kinetics
  • Molecular dynamics
  • Quantum mechanics

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