Molecular dynamics coupled with a virtual system for effective conformational sampling,Journal of Computational Chemistry

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Molecular dynamics coupled with a virtual system for effective conformational sampling
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2018-02-21 , DOI: 10.1002/jcc.25196
Tomonori Hayami ₁ , Kota Kasahara ₂ , Haruki Nakamura ₁ , Junichi Higo ₁

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An enhanced conformational sampling method is proposed: virtual‐system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free‐energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc.

中文翻译：

分子动力学与用于有效构象采样的虚拟系统相结合

提出了一种增强的构象采样方法：虚拟系统耦合经典分子动力学（VcMD）。尽管 VcMD 增强了沿反应坐标的采样，但该方法无需估计沿反应坐标的正则分布函数。这种方法引入了一个不一定遵守物理定律的虚拟系统。为了增强采样，虚拟系统与要研究的分子系统耦合。由此产生的快照会产生一个规范的集合。该方法应用于由显式溶剂中的两个短肽组成的系统。传统的分子动力学模拟比 VcMD 长十倍，与自适应伞形采样一起执行。从三个模拟计算的自由能景观相互收敛得很好。VcMD 提供比传统分子动力学更快的肽结合/解离运动。VcMD 方法因其方法简单而适用于各种复杂的系统。© 2018 Wiley Periodicals, Inc.

更新日期：2018-02-21

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