Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids.
Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids.
复制标题
DOI：
10.1021/acs.jpcb.3c03887
复制
发表时间：
2023-09-28
影响因子：
3.3
通讯作者：
Togashi, Yuichi
中科院分区：
文献类型：
--
作者：
Erban, Radek;Togashi, Yuichi
周期性边界条件通常应用于微正则 (NVE)、正则 (NVT) 和等温等压 (NpT) 系综中的分子动力学模拟。在最简单的应用中，感兴趣的生物系统被放置在溶剂化盒的中间，该溶剂化盒被选择为“足够大”，以最大限度地减少与周期性边界条件相关的任何数值伪影。这种实用方法对可模拟的生物系统的规模带来了限制。在这里，我们研究了有效无限长核酸的模拟，这些核酸在垂直于聚合物链的方向上溶剂化，同时沿着聚合物链也应用了周期性边界条件。我们研究了这些不对称周期性边界条件（APBC）对模拟结果的影响，包括生物聚合物的机械性能和周围溶剂的性能。为了进一步了解使用 APBC 的优势，首先研究了粗粒度蠕虫状链模型，说明如何从聚合物链的局部属性中提取持久长度，与一些全局平均值相比，聚合物链受 APBC 的影响较小。接下来是离子溶液中 DNA 的全原子分子动力学模拟，我们使用 APBC 来研究 DNA 分子的序列依赖性特性和周围溶剂的特性。
Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT), and isothermal–isobaric (NpT) ensembles. In their simplest application, a biological system of interest is placed in the middle of a solvation box, which is chosen ‘sufficiently large’ to minimize any numerical artifacts associated with the periodic boundary conditions. This practical approach brings limitations to the size of biological systems that can be simulated. Here, we study simulations of effectively infinitely long nucleic acids, which are solvated in the directions perpendicular to the polymer chain, while periodic boundary conditions are also applied along the polymer chain. We study the effects of these asymmetric periodic boundary conditions (APBC) on the simulated results, including the mechanical properties of biopolymers and the properties of the surrounding solvent. To get some further insights into the advantages of using the APBC, a coarse-grained worm-like chain model is first studied, illustrating how the persistence length can be extracted from the local properties of the polymer chain, which are less affected by the APBC than some global averages. This is followed by all-atom molecular dynamics simulations of DNA in ionic solutions, where we use the APBC to investigate sequence-dependent properties of DNA molecules and properties of the surrounding solvent.
登录
查看更多内容
影响因子：
8.6
作者：
Drozdetski AV;Tolokh IS;Pollack L;Baker N;Onufriev AV
通讯作者：
Onufriev AV
DOI：
10.1073/pnas.1705642114
发表时间：
2017-07-03
影响因子：
11.1
作者：
Marin-Gonzalez, Alberto;Vilhena, J. G.;Moreno-Herrero, Fernando
通讯作者：
Moreno-Herrero, Fernando
影响因子：
1.9
作者：
Erban, Radek
通讯作者：
Erban, Radek
影响因子：
2.2
作者：
Kovaleva, N. A.;Koroleva (Kikot), I. P.;Zubova, E. A.
通讯作者：
Zubova, E. A.
DOI：
10.1098/rspa.2015.0556
发表时间：
2016-02
期刊：
Proceedings. Mathematical, physical, and engineering sciences
影响因子：
--
作者：
Erban R
通讯作者：
Erban R