Molecular Dynamics Simulations on Relaxed Reduced-Dimensional Potential Energy Surfaces
Molecular Dynamics Simulations on Relaxed Reduced-Dimensional Potential Energy Surfaces
复制标题
松弛降维势能面的分子动力学模拟
DOI：
10.1021/acs.jpca.9b02298
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Jakubikova, Elena
中科院分区：
文献类型：
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作者：
Liu, Chang;Kelley, C. T.;Jakubikova, Elena
具有从高级从头计算获得的全维势能面（PES）的分子动力学（MD）模拟经常用于模拟小分子的反应动力学（即，最多有10个原子）。然而，对于较大的分子，全维PES的构建是不可行的，因为所需的从头计算的数量随着维度的增加而迅速增长。只有少量的坐标往往是必不可少的，即使是非常大的系统的反应性描述，和降维PES与这些坐标可以建立反应动力学研究。虽然基于过渡态理论框架的分析方法已经很好地建立了用于分析降维PES的方法，但是能够在这种表面上生成轨迹的MD模拟算法更加罕见。在这项工作中，我们提出了一个新的MD实现，利用放松降维PES标准微正则（NVE）和正则（NVT）MD模拟。该方法被应用到一个NH3分子的锥体反转。对从头算MD模拟，以及全维PES和实验数据的MD模拟的结果进行了验证，从MD模拟减少，三维PES。
Molecular dynamics (MD) simulations with full-dimensional potential energy surfaces (PESs) obtained from high-level ab initio calculations are frequently used to model reaction dynamics of small molecules (i.e., molecules with up to 10 atoms). Construction of full-dimensional PESs for larger molecules is, however, not feasible since the number of ab initio calculations required grows rapidly with the increase of dimension. Only a small number of coordinates are often essential for describing the reactivity of even very large systems, and reduced-dimensional PESs with these coordinates can be built for reaction dynamics studies. While analytical methods based on transition-state theory framework are well established for analyzing the reduced-dimensional PESs, MD simulation algorithms capable of generating trajectories on such surfaces are more rare. In this work, we present a new MD implementation that utilizes the relaxed reduced-dimensional PES for standard microcanonical (NVE) and canonical (NVT) MD simulations. The method is applied to the pyramidal inversion of a NH3molecule. The results from the MD simulations on a reduced, three-dimensional PES are validated against the ab initio MD simulations, as well as MD simulations on full-dimensional PES and experimental data.