Improving machine learning force fields for molecular dynamics simulations with fine-grained force metrics

被引:20
|
作者
Wang, Zun [1 ]
Wu, Hongfei [1 ]
Sun, Lixin [3 ]
He, Xinheng [1 ]
Liu, Zhirong [2 ]
Shao, Bin [1 ]
Wang, Tong [1 ]
Liu, Tie-Yan [1 ]
机构
[1] Microsoft Res AI4Sci, Beijing 100084, Peoples R China
[2] Peking Univ, Coll Chem & Mol Engn, Beijing 100871, Peoples R China
[3] Microsoft Res AI4Sci, Cambridge CB1 2FB, England
来源
JOURNAL OF CHEMICAL PHYSICS | 2023年 / 159卷 / 03期
关键词
Atoms - Conformations - Cost effectiveness - Molecular dynamics - Molecules;
D O I
10.1063/5.0147023
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Machine learning force fields (MLFFs) have gained popularity in recent years as they provide a cost-effective alternative to ab initio molecular dynamics (MD) simulations. Despite a small error on the test set, MLFFs inherently suffer from generalization and robustness issues during MD simulations. To alleviate these issues, we propose global force metrics and fine-grained metrics from element and conformation aspects to systematically measure MLFFs for every atom and every conformation of molecules. We selected three state-of-the-art MLFFs (ET, NequIP, and ViSNet) and comprehensively evaluated on aspirin, Ac-Ala3-NHMe, and Chignolin MD datasets with the number of atoms ranging from 21 to 166. Driven by the trained MLFFs on these molecules, we performed MD simulations from different initial conformations, analyzed the relationship between the force metrics and the stability of simulation trajectories, and investigated the reason for collapsed simulations. Finally, the performance of MLFFs and the stability of MD simulations can be further improved guided by the proposed force metrics for model training, specifically training MLFF models with these force metrics as loss functions, fine-tuning by reweighting samples in the original dataset, and continued training by recruiting additional unexplored data.
引用
收藏
页数:12
相关论文
共 50 条
  • [1] Machine Learning of Coarse-Grained Molecular Dynamics Force Fields
    Wang, Jiang
    Olsson, Simon
    Wehmeyer, Christoph
    Perez, Adria
    Charron, Nicholas E.
    de Fabritiis, Gianni
    Noe, Frank
    Clementi, Cecilia
    ACS CENTRAL SCIENCE, 2019, 5 (05) : 755 - 767
  • [2] Machine learning of coarse-grained molecular dynamics force fields
    Noe, Frank
    Clementi, Cecilia
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2019, 258
  • [3] Force fields and molecular dynamics simulations
    Gonzalez, M. A.
    NEUTRONS ET SIMULATIONS, JDN 18, 2010, : 169 - 200
  • [4] Machine Learning for Accurate Force Calculations in Molecular Dynamics Simulations
    Pattnaik, Punyaslok
    Raghunathan, Shampa
    Kalluri, Tarun
    Bhimalapuram, Prabhakar
    Jawahar, C., V
    Priyakumar, U. Deva
    JOURNAL OF PHYSICAL CHEMISTRY A, 2020, 124 (34): : 6954 - 6967
  • [5] Simulations and force fields with quantum mechanics/molecular mechanics and machine learning
    Yang, Weitao
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2019, 258
  • [6] Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields
    McDonagh, James L.
    Shkurti, Ardita
    Bray, David J.
    Anderson, Richard L.
    Pyzer-Knapp, Edward O.
    JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2019, 59 (10) : 4278 - 4288
  • [7] Towards exact molecular dynamics simulations with machine-learned force fields
    Chmiela, Stefan
    Sauceda, Huziel
    Mueller, Klaus-Robert
    Tkatchenko, Alexandre
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2018, 256
  • [8] Towards exact molecular dynamics simulations with machine-learned force fields
    Chmiela, Stefan
    Sauceda, Huziel E.
    Mueller, Klaus-Robert
    Tkatchenko, Alexandre
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2019, 257
  • [9] Towards exact molecular dynamics simulations with machine-learned force fields
    Chmiela, Stefan
    Sauceda, Huziel E.
    Mueller, Klaus-Robert
    Tkatchenko, Alexandre
    NATURE COMMUNICATIONS, 2018, 9
  • [10] Towards exact molecular dynamics simulations with machine-learned force fields
    Stefan Chmiela
    Huziel E. Sauceda
    Klaus-Robert Müller
    Alexandre Tkatchenko
    Nature Communications, 9