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arxiv_ai 97% Match Research paper Computational chemists,Materials scientists,Drug discovery researchers,Biophysicists,ML researchers in scientific domains 1 week ago

Artificial Intelligence for Direct Prediction of Molecular Dynamics Across Chemical Space

graph-neural-networks › molecular-modeling
📄 Abstract

Abstract: Molecular dynamics (MD) is a powerful tool for exploring the behavior of atomistic systems, but its reliance on sequential numerical integration limits simulation efficiency. We present a novel neural network architecture, MDtrajNet, and a pre-trained foundational model, MDtrajNet-1, that directly generates MD trajectories across chemical space, bypassing force calculations and integration. This approach accelerates simulations by up to two orders of magnitude compared to traditional MD, even those enhanced by machine-learning interatomic potentials. MDtrajNet combines equivariant neural networks with a transformer-based architecture to achieve strong accuracy and transferability in predicting long-time trajectories. Remarkably, the errors of the trajectories generated by MDtrajNet-1 for various known and unseen molecular systems are close to those of the conventional ab initio MD. The architecture's flexible design supports diverse application scenarios, including different statistical ensembles, boundary conditions, and interaction types. By overcoming the intrinsic speed barrier of conventional MD, MDtrajNet opens new frontiers in efficient and scalable atomistic simulations.
Authors (2)
Fuchun Ge
Pavlo O. Dral
Submitted
May 22, 2025
arXiv Category
physics.chem-ph
arXiv PDF

Key Contributions

Introduces MDtrajNet, a novel neural network architecture and foundational model that directly generates molecular dynamics trajectories, bypassing traditional force calculations and integration. This approach achieves up to two orders of magnitude acceleration compared to conventional MD methods, with accuracy comparable to ab initio MD, enabling efficient exploration of chemical space.

Business Value

Dramatically accelerates drug discovery, materials design, and understanding of chemical processes by enabling faster and more extensive molecular simulations.