ArticlePhilosophical transactions. Series A, Mathematical, physical, and engineering sciences2014
Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.
Article in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Mechanical Unfolding of Proteins-A Comparative Nonequilibrium Molecular Dynamics Study.Biophysical journal · 2020Article
- Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices.Chemical science · 2019Article
- A Trajectory-Based Method to Explore Reaction Mechanisms.Molecules (Basel, Switzerland) · 2018Review
- Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation.FEBS open bio · 2017Article
- A Blind Test of Computational Technique for Predicting the Likelihood of Peptide Sequences to Cyclize.The journal of physical chemistry letters · 2017Article
- An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis.Chemical science · 2017Article
- Multiscale modelling: approaches and challenges.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2014Article
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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.
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