An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.
An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.
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DOI：
10.1021/acs.chemrev.5b00505
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发表时间：
2016-05-11
期刊：
影响因子：
62.1
通讯作者：
MacKerell AD Jr
中科院分区：
文献类型：
--
作者：
Lemkul JA;Huang J;Roux B;MacKerell AD Jr
明确解释诱导极化的分子力学力场代表了分子动力学模拟的下一代物理模型。有几种方法存在建模诱导极化，在这里，我们回顾了经典的Drude振荡器模型，其中电子自由度的模型由带电粒子附着在其核心原子的核谐波弹簧。我们描述了德鲁德力场参数化和应用的最新发展，主要是在过去的15年。重点放在Drude-2013蛋白质，DNA，脂质和碳水化合物的极化力场上。我们讨论了它的参数化协议，发展历史和最近的模拟生物有趣的系统，突出的具体研究中，激发极化在再现实验观测和理解物理行为中起着至关重要的作用。由于德鲁德振荡器模型在计算上易于处理，并且可以在广泛的模拟包中使用，因此预计使用这些更复杂的物理模型将导致对驱动一系列化学和生物现象的物理力的新的重要发现。
Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena.