Wells David B, Bhattacharya Swati, Carr Rogan, Maffeo Christopher, Ho Anthony, Comer Jeffrey, Aksimentiev Aleksei
Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Methods Mol Biol. 2012;870:165-86. doi: 10.1007/978-1-61779-773-6_10.
Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA-ion interactions, and the ionic current through a nanopore.
分子动力学（MD）模拟已成为合理设计和解释DNA通过纳米孔转位实验研究的标准方法。然而，MD方法提供了多种算法、参数和其他协议选择，这些都会影响所得数据的准确性以及计算效率。在本章中，我们研究了MD方法提供的最常用选择，寻求一组最优参数，以实现对DNA和离子通过生物纳米孔传输进行计算效率最高且最准确的模拟。特别是，我们研究了短程截止、积分时间步长和力场参数对体离子电导率、离子配对、离子溶剂化能、DNA结构、DNA-离子相互作用以及通过纳米孔的离子电流的温度和浓度依赖性的影响。
