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Refining potential energy surface through dynamical properties via differentiable molecular simulation

Author

Listed:
  • Bin Han

    (Tsinghua Shenzhen International Graduate School (TSIGS))

  • Kuang Yu

    (Tsinghua Shenzhen International Graduate School (TSIGS))

Abstract

Recently, machine learning potential (MLP) largely enhances the reliability of molecular dynamics, but its accuracy is limited by the underlying ab initio methods. A viable approach to overcome this limitation is to refine the potential by learning from experimental data, which now can be done efficiently using modern automatic differentiation technique. However, potential refinement is mostly performed using thermodynamic properties, leaving the most accessible and informative dynamical data (like spectroscopy) unexploited. In this work, through a comprehensive application of adjoint and gradient truncation methods, we show that both memory and gradient explosion issues can be circumvented in many situations, so the dynamical property differentiation is well-behaved. Consequently, both transport coefficients and spectroscopic data can be used to improve the density functional theory based MLP towards higher accuracy. Essentially, this work contributes to the solution of the inverse problem of spectroscopy by extracting microscopic interactions from vibrational spectroscopic data.

Suggested Citation

  • Bin Han & Kuang Yu, 2025. "Refining potential energy surface through dynamical properties via differentiable molecular simulation," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56061-z
    DOI: 10.1038/s41467-025-56061-z
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    References listed on IDEAS

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    1. Simon Batzner & Albert Musaelian & Lixin Sun & Mario Geiger & Jonathan P. Mailoa & Mordechai Kornbluth & Nicola Molinari & Tess E. Smidt & Boris Kozinsky, 2022. "E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Peter Eastman & Jason Swails & John D Chodera & Robert T McGibbon & Yutong Zhao & Kyle A Beauchamp & Lee-Ping Wang & Andrew C Simmonett & Matthew P Harrigan & Chaya D Stern & Rafal P Wiewiora & Bernar, 2017. "OpenMM 7: Rapid development of high performance algorithms for molecular dynamics," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-17, July.
    3. Justin S. Smith & Benjamin T. Nebgen & Roman Zubatyuk & Nicholas Lubbers & Christian Devereux & Kipton Barros & Sergei Tretiak & Olexandr Isayev & Adrian E. Roitberg, 2019. "Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning," Nature Communications, Nature, vol. 10(1), pages 1-8, December.
    4. Stephan Thaler & Julija Zavadlav, 2021. "Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    5. Yaolong Zhang & Bin Jiang, 2023. "Universal machine learning for the response of atomistic systems to external fields," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
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