# ATOM: A Pretrained Neural Operator for Multitask Molecular Dynamics

arXiv: https://arxiv.org/abs/2510.05482 · HTML: https://mlsanity.com/paper/2510.05482/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 51 of its 89 references that are in the map.
- First posted on arXiv 7 Oct 2025.

## Builds on (most cited first, 30 of 51)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Fourier Neural Operator for Parametric Partial Differential Equations](https://mlsanity.com/paper/2010.08895/) (2020)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges](https://mlsanity.com/paper/2104.13478/) (2021)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [Scheduled Sampling for Sequence Prediction with Recurrent Neural Networks](https://mlsanity.com/paper/1506.03099/) (2015)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [PointConv: Deep Convolutional Networks on 3D Point Clouds](https://mlsanity.com/paper/1811.07246/) (2018)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Neural Operator: Learning Maps Between Function Spaces](https://mlsanity.com/paper/2108.08481/) (2021)
- [3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data](https://mlsanity.com/paper/1807.02547/) (2018)
- [GNOT: A General Neural Operator Transformer for Operator Learning](https://mlsanity.com/paper/2302.14376/) (2023)
- [Graph Neural Networks with Learnable Structural and Positional Representations](https://mlsanity.com/paper/2110.07875/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [Learning Local Equivariant Representations for Large-Scale Atomistic Dynamics](https://mlsanity.com/paper/2204.05249/) (2022)
- [Learning Gradient Fields for Molecular Conformation Generation](https://mlsanity.com/paper/2105.03902/) (2021)
- [Graph Inductive Biases in Transformers without Message Passing](https://mlsanity.com/paper/2305.17589/) (2023)
- [DPOT: Auto-Regressive Denoising Operator Transformer for Large-Scale PDE Pre-Training](https://mlsanity.com/paper/2403.03542/) (2024)
- [Label Noise SGD Provably Prefers Flat Global Minimizers](https://mlsanity.com/paper/2106.06530/) (2021)
- [Equivariance with Learned Canonicalization Functions](https://mlsanity.com/paper/2211.06489/) (2022)
- [The Design Space of E(3)-Equivariant Atom-Centered Interatomic Potentials](https://mlsanity.com/paper/2205.06643/) (2022)
- [Shape Matters: Understanding the Implicit Bias of the Noise Covariance](https://mlsanity.com/paper/2006.08680/) (2020)
- [SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials](https://mlsanity.com/paper/2209.10702/) (2022)
- [Equivariant Graph Mechanics Networks with Constraints](https://mlsanity.com/paper/2203.06442/) (2022)
- [Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics](https://mlsanity.com/paper/2302.01170/) (2023)

## Built on by (most cited first, 1 of 1)

- [Learning Hamiltonian Flow Maps: Mean Flow Consistency for Large-Timestep Molecular Dynamics](https://mlsanity.com/paper/2601.22123/) (2026)

## Abstract (arXiv)

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.