Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step
Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step
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DOI：
10.1021/acs.jctc.8b00874
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发表时间：
2019-01-01
影响因子：
5.5
通讯作者：
Sugita, Yuji
中科院分区：
文献类型：
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作者：
Jung, Jaewoon;Kobayashi, Chigusa;Sugita, Yuji
在分子动力学 (MD) 模拟中，准确评估温度对于控制等温等压条件下的温度和压力至关重要。根据托尔曼均分定理，所有粒子的所有运动都应共享一个温度。然而，传统的动能温度估计并未正确包含Hessian项，因此，大时间步长时不满足均分定理。在本文中，我们展示了如何在不增加计算成本的情况下最准确地评估温度。我们定义了两种动能，分别在低估或高估温度的全时和半时步长处进行评估。这两种动能的组合提供了高达三阶时间步长的最佳瞬时温度。该方法针对一维谐振子、纯水分子、水分子中的牛胰蛋白酶抑制剂 (BPTI) 蛋白以及水分子中的水合 1,2-二棕榈酰-sn-磷脂酰胆碱 (DPPC) 脂质双层进行了测试。在所有测试中，最佳温度估计器比现有方法更好地满足均分定理，并且在时间步长达到（包括 5 fs）时很好地再现了通常的物理特性。
In molecular dynamics (MD) simulations, an accurate evaluation of temperature is essential for controlling temperature as well as pressure in the isothermal-isobaric conditions. According to the Tolman's equipartition theorem, all motions of all particles should share a single temperature. However, conventional temperature estimation from kinetic energy does not include Hessian terms properly, and thereby, the equipartition theorem is not satisfied with a large time step. In this paper, we show how to evaluate temperature the most accurately without increasing computational cost. We define two kinds of kinetic energies, evaluated at full- and half-time steps that underestimate or overestimate temperature, respectively. A combination of these two kinetic energies provides an optimal instantaneous temperature up to the third order of the time step. The method is tested for a one-dimensional harmonic oscillator, pure water molecules, a Bovine pancreatic trypsin inhibitor (BPTI) protein in water molecules, and a hydrated 1,2-dispalmitoyl-sn-phosphatidylcholine (DPPC) lipid bilayer in water molecules. In all tests, the optimal temperature estimator fulfills the equipartition theorem better than existing methods and reproduces well the usual physical properties for time steps up to and including 5 fs.