ATOM: A Pretrained Neural Operator for Multitask Molecular Dynamics

Abstract

Molecular dynamics (MD) simulations underpin modern computational drug discovery, materials science, and biochemistry. Recent machine learning models provide high-fidelity MD predictions without the need to repeatedly solve quantum mechanical forces, enabling significant speedups over conventional pipelines. Yet many such methods typically enforce strict equivariance and rely on sequential rollouts, thus limiting their flexibility and simulation efficiency. They are also commonly single-task, trained on individual molecules and fixed timeframes, which restricts generalization to unseen compounds and extended timesteps. To address these issues, we propose Atomistic Transformer Operator for Molecules (ATOM), a pretrained transformer neural operator for multitask molecular dynamics. ATOM adopts a quasi-equivariant design that requires no explicit molecular graph and employs a temporal attention mechanism, allowing for the accurate parallel decoding of multiple future states. To support operator pretraining across chemicals and timescales, we curate TG80, a large, diverse, and numerically stable MD dataset with over 2.5 million femtoseconds of trajectories across 80 compounds. ATOM achieves state-of-the-art performance on established single-task benchmarks, such as MD17, RMD17 and MD22. After multitask pretraining on TG80, ATOM shows exceptional zero-shot generalization to unseen molecules across varying time horizons. We believe ATOM represents a significant step toward accurate, efficient, and transferable molecular dynamics models.