期刊
出版社
ROYAL SOC
DOI: 10.1098/rsta.2013.0384
关键词
molecular dynamics; quantum mechanics; dynamics of proteins; chemical dynamics; kinetics
资金
- Royal Society Research Fellowship
- EPSRC [EP/E009824/1]
- 'Ministerio de Economia y Competitividad' [CTQ2009-12588]
- Leverhulme Trust [VP1-2012-013]
- EPSRC [EP/E009824/1, EP/J001481/1, EP/I014500/1] Funding Source: UKRI
- Engineering and Physical Sciences Research Council [EP/E009824/1, EP/J001481/1, EP/I014500/1] Funding Source: researchfish
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 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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据