Reactive molecular dynamics: From small molecules to proteins,Wiley Interdisciplinary Reviews: Computational Molecular Science

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Reactive molecular dynamics: From small molecules to proteins
Wiley Interdisciplinary Reviews: Computational Molecular Science ( IF 16.8 ) Pub Date : 2018-08-24 , DOI: 10.1002/wcms.1386
Markus Meuwly _{1,

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Affiliation

The current status of reactive molecular dynamics (MD) simulations is summarized. Both, methodological aspects and applications to problems ranging from gas phase reaction dynamics to ligand‐binding in solvated proteins are discussed, focusing on extracting information from simulations that cannot easily be obtained from experiments alone. One specific example is the structural interpretation of the ligand rebinding time scales extracted from state‐of‐the art time‐resolved experiments. Atomistic simulations employing validated reactive interaction potentials are capable of providing structural information about the time scales involved. Both, merits and shortcomings of the various methods are discussed and the outlook summarizes possible future avenues such as reactive potentials based on machine learning techniques.

中文翻译：

反应分子动力学：从小分子到蛋白质

总结了反应分子动力学（MD）模拟的当前状态。从气相反应动力学到溶剂化蛋白质中配体结合的问题，方法学方面以及方法论方面的问题都得到了讨论，重点是从模拟中提取信息，而这些信息是很难单独从实验中获得的。一个具体的例子是从最新的时间分辨实验中提取的配体重新结合时间尺度的结构解释。采用已验证的反应性相互作用势的原子模拟能够提供有关所涉及时间尺度的结构信息。讨论了各种方法的优缺点，并且展望总结了未来的可能途径，例如基于机器学习技术的无功电势。

更新日期：2018-08-24

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