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基于支持向量回归的柔性水团簇蒙特卡罗模拟

Support Vector Regression-Based Monte Carlo Simulation of Flexible Water Clusters.

作者信息

Bose Samik, Chakrabarty Suman, Ghosh Debashree

机构信息

School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, West Bengal, India.

Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India.

出版信息

ACS Omega. 2020 Mar 24;5(13):7065-7073. doi: 10.1021/acsomega.9b02968. eCollection 2020 Apr 7.

Abstract

Molecular simulations based on classical force fields are computationally efficient but lack accuracy due to the empirical formulation of non-bonded interactions. Quantum mechanical (QM) methods, albeit accurate, have inhibitory computational costs for large molecules and clusters. Hence, to overcome the bottleneck, machine learning (ML)-based methods have been employed in the recent years. We had earlier reported a combined scheme of many-body expansion (MBE) and ML to predict the interaction energies of rigid water clusters. In this work, we proceed toward building a flexible water model using the ML-MBE scheme. This ML-MBE scheme has an error of <1% for interaction energy prediction in comparison to the parent QM method for flexible water decamers. Machine learning-based Monte Carlo simulations (MLMC) are performed with this water model, and the structural properties of these configurations are compared with those obtained from ab initio molecular dynamics (AIMD) and the TIP3P classical force field. The radial distribution functions, tetrahedral order parameters, and number of hydrogen bonds in AIMD and MLMC have a similar qualitative and quantitative trend, whereas the classical force fields show a significant deviation.

摘要

基于经典力场的分子模拟计算效率高,但由于非键相互作用的经验公式化,缺乏准确性。量子力学(QM)方法虽然准确,但对于大分子和团簇来说计算成本过高。因此,为了克服这一瓶颈,近年来采用了基于机器学习(ML)的方法。我们之前报道了一种多体展开(MBE)和ML相结合的方案,用于预测刚性水团簇的相互作用能。在这项工作中,我们着手使用ML-MBE方案构建一个灵活的水模型。与用于灵活水十聚体的母体QM方法相比,这种ML-MBE方案在相互作用能预测方面的误差小于1%。使用这个水模型进行基于机器学习的蒙特卡罗模拟(MLMC),并将这些构型的结构性质与从头算分子动力学(AIMD)和TIP3P经典力场得到的结构性质进行比较。AIMD和MLMC中的径向分布函数、四面体序参数和氢键数量具有相似的定性和定量趋势,而经典力场则显示出显著偏差。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8397/7143414/996188a31b81/ao9b02968_0011.jpg

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