Confronting pitfalls of AI-augmented molecular dynamics using statistical physics

Shashank Pant, Zachary Smith, Yihang Wang, Emad Tajkhorshid, Pratyush Tiwary

Research output: Contribution to journalArticlepeer-review


Artificial intelligence (AI)-based approaches have had indubitable impact across the sciences through the ability to extract relevant information from raw data. Recently, AI has also found use in enhancing the efficiency of molecular simulations, wherein AI derived slow modes are used to accelerate the simulation in targeted ways. However, while typical fields where AI is used are characterized by a plethora of data, molecular simulations, per construction, suffer from limited sampling and thus limited data. As such, the use of AI in molecular simulations can suffer from a dangerous situation where the AI-optimization could get stuck in spurious regimes, leading to incorrect characterization of the reaction coordinate (RC) for the problem at hand. When such an incorrect RC is then used to perform additional simulations, one could start to deviate progressively from the ground truth. To deal with this problem of spurious AI-solutions, here, we report a novel and automated algorithm using ideas from statistical mechanics. It is based on the notion that a more reliable AI-solution will be one that maximizes the timescale separation between slow and fast processes. To learn this timescale separation even from limited data, we use a maximum caliber-based framework. We show the applicability of this automatic protocol for three classic benchmark problems, namely, the conformational dynamics of a model peptide, ligand-unbinding from a protein, and folding/unfolding energy landscape of the C-terminal domain of protein G. We believe that our work will lead to increased and robust use of trustworthy AI in molecular simulations of complex systems.

Original languageEnglish (US)
Pages (from-to)234118
Number of pages1
JournalThe Journal of Chemical Physics
Issue number23
StatePublished - Dec 21 2020

ASJC Scopus subject areas

  • General Physics and Astronomy
  • Physical and Theoretical Chemistry


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