Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.
Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.
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DOI：
10.1098/rspa.2015.0556
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发表时间：
2016-02
期刊：
影响因子：
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通讯作者：
Erban R
中科院分区：
文献类型：
--
作者：
Erban R
研究了水溶液中离子（K+, Na+， Ca2+和Cl−）的分子动力学（MD）模拟。水的描述使用SPC/E模型。提出了一种离子行为的随机粗粒度描述，并使用MD模拟进行了参数化。它是一个描述离子位置、速度和加速度的随机和常微分耦合方程组。随机粗粒度模型提供了一种介于全原子MD模拟和布朗动力学（BD）模型之间的中间描述。它被用于开发一种多尺度方法，该方法在部分计算域中使用全原子MD模拟，而在其余域中使用（不太详细的）BD模拟。
Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.