Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation,The Journal of Physical Chemistry B

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Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2018-02-13 00:00:00 , DOI: 10.1021/acs.jpcb.7b10830
Kota Kasahara ₁ , Shun Sakuraba ₂ , Ikuo Fukuda ₃

Affiliation

We investigate the problem of artifacts caused by the periodic boundary conditions (PBC) used in molecular simulation studies. Despite the long history of simulations with PBCs, the existence of measurable artifacts originating from PBCs applied to inherently nonperiodic physical systems remains controversial. Specifically, these artifacts appear as differences between simulations of the same system but with different simulation-cell sizes. Earlier studies have implied that, even in the simple case of a small model peptide in water, sampling inefficiency is a major obstacle to understanding these artifacts. In this study, we have resolved the sampling issue using the replica exchange molecular dynamics (REMD) enhanced-sampling method to explore PBC artifacts. Explicitly solvated zwitterionic polyalanine octapeptides with three different cubic-cells, having dimensions of L = 30, 40, and 50 Å, were investigated to elucidate the differences with 64 replica × 500 ns REMD simulations using the AMBER parm99SB force field. The differences among them were not large overall, and the results for the L = 30 and 40 Å simulations in the conformational free energy landscape were found to be very similar at room temperature. However, a small but statistically significant difference was seen for L = 50 Å. We observed that extended conformations were slightly overstabilized in the smaller systems. The origin of these artifacts is discussed by comparison to an electrostatic calculation method without PBCs.

中文翻译：

聚丙氨酸八肽分子动力学模拟的增强采样：周期性边界条件对肽构象的影响。

我们调查由分子模拟研究中使用的周期性边界条件（PBC）引起的伪影问题。尽管使用PBC进行模拟的历史悠久，但存在源自PBC的可测量伪像应用于固有的非周期性物理系统仍存在争议。具体来说，这些伪像表现为同一系统的仿真之间的差异，但仿真单元的大小不同。较早的研究表明，即使在水中有小模型肽的简单情况下，采样效率低下也是理解这些假象的主要障碍。在这项研究中，我们已经解决了使用副本交换分子动力学（REMD）增强采样方法探索PBC伪像的采样问题。显式溶剂化的两性离子聚丙氨酸八肽，具有三个不同的立方细胞，尺寸为L使用AMBER parm99SB力场研究了30、40和50Å，以阐明64个复制品×500 ns REMD仿真的差异。它们之间的总体差异并不大，在构象自由能态下，L = 30和40Å模拟的结果在室温下非常相似。但是，对于L = 50Å ，可以看到很小但具有统计学意义的差异。我们观察到，在较小的系统中，扩展的构象稍微不稳定。通过与无PBC的静电计算方法进行比较，讨论了这些伪影的起源。

更新日期：2018-02-13

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