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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.

DOI:10.1021/acsomega.9b02968
PMID:32280847
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7143414/
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/d3b18fe3cd0d/ao9b02968_0002.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8397/7143414/580c349f2ad8/ao9b02968_0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8397/7143414/8b65c417d9ce/ao9b02968_0007.jpg
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本文引用的文献

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2
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Chem Sci. 2017 Jul 1;8(7):5137-5152. doi: 10.1039/c7sc01247k. Epub 2017 May 17.
3
Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions.
比较置换不变多项式、神经网络和高斯逼近势在通过多体展开表示水分子相互作用中的表现。
J Chem Phys. 2018 Jun 28;148(24):241725. doi: 10.1063/1.5024577.
4
Force Field Parametrization of Metal Ions from Statistical Learning Techniques.基于统计学习技术的金属离子力场参数化
J Chem Theory Comput. 2018 Jan 9;14(1):255-273. doi: 10.1021/acs.jctc.7b00779. Epub 2017 Dec 6.
5
Toward chemical accuracy in the description of ion-water interactions through many-body representations. Alkali-water dimer potential energy surfaces.通过多体表示方法实现离子-水相互作用的化学精度描述。碱-水二聚体势能面。
J Chem Phys. 2017 Oct 28;147(16):161715. doi: 10.1063/1.4993213.
6
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J Chem Theory Comput. 2017 Sep 12;13(9):4492-4503. doi: 10.1021/acs.jctc.7b00521. Epub 2017 Sep 1.
7
Hidden electrostatic basis of dynamic allostery in a PDZ domain.PDZ 域中动态变构的隐藏静电基础。
Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E5825-E5834. doi: 10.1073/pnas.1705311114. Epub 2017 Jun 20.
8
Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach.静电起源于 RNA 螺旋体中 DFHBDI 的红溶剂化变色。
J Phys Chem B. 2017 May 11;121(18):4790-4798. doi: 10.1021/acs.jpcb.7b02445. Epub 2017 May 2.
9
On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice.关于水的MB-pol多体势的准确性:从团簇到液态水和冰的相互作用能、振动频率以及经典热力学和动力学性质
J Chem Phys. 2016 Nov 21;145(19):194504. doi: 10.1063/1.4967719.
10
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