机器学习原子间相互作用建模
MOLECULAR MODELING BY MACHIN LEARNING
查看参考文献109篇
文摘
|
原子间相互作用建模是分子动力学模拟的核心问题之一.基于第一性原理的建模准而不快,经验势模型快而不准,因此人们长期面临精度和效率只得其一的两难困境.基于机器学习的原子间相互作用建模在达到第一性原理精度的同时,计算开销大大降低,因而有希望解决这一两难困境.本文将介绍构造基于机器学习的原子间相互作用模型的一般框架,归纳近年来的主要建模工作,并探讨这些工作的优势和劣势. |
其他语种文摘
|
Modeling the interatomic potential is one of the crucial problems in the field of molecular simulation. For a long time, the community faces the dilemma that the first-principles calculations are accurate but slow, while the empirical force fields are efficient but inaccurate. Machine learning is a promising approach to solve the dilemma because it achieves comparable accuracy with the first-principles calculations at a much lower expense. In this review, we present a general framework for developing the machine learning interatomic potentials, provide an incomplete list of recent work in this direction, and investigate the advantages and disadvantages of the reviewed approaches. |
来源
|
计算数学
,2021,43(3):261-278 【核心库】
|
DOI
|
10.12286/jssx.j2021-0833
|
关键词
|
机器学习
;
原子间作用势
;
分子动力学模拟
|
地址
|
1.
北京应用物理与计算数学研究所计算物理实验室, 北京, 100094
2.
北京大学工学院应用物理与技术中心, 北京, 100871
|
语种
|
中文 |
文献类型
|
研究性论文 |
ISSN
|
0254-7791 |
学科
|
数学 |
基金
|
国家自然科学基金
|
文献收藏号
|
CSCD:7118700
|
参考文献 共
109
共6页
|
1.
Abrams C. Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration.
Entropy,2014,16(1):163-199
|
CSCD被引
8
次
|
|
|
|
2.
Bernardi R C. Enhanced sampling techniques in molecular dynamics simulations of biological systems.
Biochimica et Biophysica Acta (BBA)-General Subjects,2015,1850(5):872-877
|
CSCD被引
13
次
|
|
|
|
3.
Yang Y I. Enhanced sampling in molecular dynamics.
The Journal of chemical physics,2019,151(7):070902
|
CSCD被引
6
次
|
|
|
|
4.
Born M. Zur quantentheorie der molekeln.
Annalen der physik,1927,389(20):457-484
|
CSCD被引
35
次
|
|
|
|
5.
Schrodinger E. An undulatory theory of the mechanics of atoms and molecules.
Physical review,1926,28(6):1049
|
CSCD被引
20
次
|
|
|
|
6.
Hohenberg P. Inhomogeneous electron gas.
Physical review,1964,136(3B):B864
|
CSCD被引
1092
次
|
|
|
|
7.
Kohn W. Self-consistent equations including exchange and correlation effects.
Physical review,1965,140(4A):A1133
|
CSCD被引
1328
次
|
|
|
|
8.
Moller C. Note on an approximation treatment for many-electron systems.
Physical review,1934,46(7):618
|
CSCD被引
65
次
|
|
|
|
9.
Cizek J. On the correlation problem in atomic and molecular systems. Calculation of wave-function components in Ursell-type expansion using quantum-field theoretical methods.
The Journal of Chemical Physics,1966,45(11):4256-4266
|
CSCD被引
7
次
|
|
|
|
10.
Car R. Unified approach for molecular dynamics and density-functional theory.
Physical review letters,1985,55(22):2471
|
CSCD被引
167
次
|
|
|
|
11.
Daura X. Parametrization of aliphatic CHn united atoms of GROMOS96 force field.
Journal of Computational Chemistry,1998,19(5):535-547
|
CSCD被引
8
次
|
|
|
|
12.
Schuler L D. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase.
Journal of Computational Chemistry,2001,22(11):1205-1218
|
CSCD被引
9
次
|
|
|
|
13.
MacKerell A. All-atom empirical potential for molecular modeling and dynamics studies of proteins.
The Journal of Physical Chemistry B,1998,102(18):3586-3616
|
CSCD被引
136
次
|
|
|
|
14.
Vanommeslaeghe K. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
Journal of computational chemistry,2010,31(4):671-690
|
CSCD被引
36
次
|
|
|
|
15.
MacKerell A D. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
Journal of computational chemistry,2004,25(11):1400-1415
|
CSCD被引
23
次
|
|
|
|
16.
Yu Y. CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids.
Journal of Chemical Theory and Computation,2021
|
CSCD被引
1
次
|
|
|
|
17.
Wang J. Development and testing of a general amber force field.
Journal of computational chemistry,2004,25(9):1157-1174
|
CSCD被引
122
次
|
|
|
|
18.
Hornak V. Comparison of multiple Amber force fields and development of improved protein backbone parameters.
Proteins: Structure, Function, and Bioinformatics,2006,65(3):712-725
|
CSCD被引
48
次
|
|
|
|
19.
Lindorff-Larsen K. Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Proteins: Structure, Function, and Bioinformatics,2010,78(8):1950-1958
|
CSCD被引
55
次
|
|
|
|
20.
Jorgensen W. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids.
Journal of the American Chemical Society,1996,118(45):11225-11236
|
CSCD被引
192
次
|
|
|
|
|