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一种用于超高压分子动力学模拟的算法。

An algorithm for very high pressure molecular dynamics simulations.

作者信息

Tesi Marina, Cammi Roberto, Granucci Giovanni, Persico Maurizio

机构信息

Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy.

Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parma, Italy.

出版信息

J Comput Chem. 2024 Dec 15;45(32):2848-2861. doi: 10.1002/jcc.27461. Epub 2024 Aug 29.

DOI:10.1002/jcc.27461
PMID:39207220
Abstract

We describe a method to run simulations of ground or excited state dynamics under extremely high pressures. The method is based on the introduction of a fictitious ideal gas that exerts the required pressure on a molecular sample and is therefore called XP-GAS (eXtreme Pressure by Gas Atoms in a Sphere). The algorithm is most suitable for approximately spherical clusters of molecules described by quantum chemistry methods, Molecular Mechanics or mixed QM/MM approaches. We compare the results obtained by the algorithm here presented and by the XP-PCM approach, based on a continuum description of the environment. As a test case, we study the conformational dynamics of 1,3-butadiene either as an isolated molecule ("naked" butadiene) or embedded in a cluster of argon atoms, under pressures up to 15 GPa. Overall, our results show that the XP-GAS QM/MM simulation method is in good agreement with the XP-PCM QM/Continuum model (Cammi model) in describing the effect of the pressure on static properties as the equilibrium geometry of butadiene in the ground state. Furthermore, the comparison of XP-GAS simulations with naked butadiene and butadiene in argon shows the importance, for XP-GAS and related methods, of a realistic representation of the medium in modelling pressure effects.

摘要

我们描述了一种在极高压力下运行基态或激发态动力学模拟的方法。该方法基于引入一种虚拟理想气体,它对分子样本施加所需的压力,因此被称为XP-GAS(球体中气体原子产生的极端压力)。该算法最适用于通过量子化学方法、分子力学或混合QM/MM方法描述的近似球形分子簇。我们将这里提出的算法所获得的结果与基于环境连续描述的XP-PCM方法所获得的结果进行了比较。作为一个测试案例,我们研究了1,3-丁二烯作为孤立分子(“裸”丁二烯)或嵌入氩原子簇中的构象动力学,压力高达15 GPa。总体而言,我们的结果表明,在描述压力对静态性质(如基态丁二烯的平衡几何结构)的影响方面,XP-GAS QM/MM模拟方法与XP-PCM QM/连续介质模型(卡米模型)高度一致。此外,XP-GAS对裸丁二烯和氩中丁二烯的模拟比较表明,对于XP-GAS及相关方法而言,在模拟压力效应时对介质进行真实表征非常重要。

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