# Align Your Structures: Generating Trajectories with Structure Pretraining for Molecular Dynamics

arXiv: https://arxiv.org/abs/2604.03911 · HTML: https://mlsanity.com/paper/2604.03911/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 61 references that are in the map.
- First posted on arXiv 5 Apr 2026.

## Builds on (most cited first, 21 of 21)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Align your Latents: High-Resolution Video Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2304.08818/) (2023)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [Learning from Protein Structure with Geometric Vector Perceptrons](https://mlsanity.com/paper/2009.01411/) (2020)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [Geometric and Physical Quantities Improve E(3) Equivariant Message Passing](https://mlsanity.com/paper/2110.02905/) (2021)
- [TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials](https://mlsanity.com/paper/2202.02541/) (2022)
- [Learning Gradient Fields for Molecular Conformation Generation](https://mlsanity.com/paper/2105.03902/) (2021)
- [AlphaFold Meets Flow Matching for Generating Protein Ensembles](https://mlsanity.com/paper/2402.04845/) (2024)
- [GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles](https://mlsanity.com/paper/2106.07802/) (2021)
- [Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics](https://mlsanity.com/paper/2302.01170/) (2023)
- [Generative Modeling of Molecular Dynamics Trajectories](https://mlsanity.com/paper/2409.17808/) (2024)
- [Geometry-Complete Diffusion for 3D Molecule Generation and Optimization](https://mlsanity.com/paper/2302.04313/) (2023)
- [EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants](https://mlsanity.com/paper/2410.09667/) (2024)
- [Geometric Trajectory Diffusion Models](https://mlsanity.com/paper/2410.13027/) (2024)
- [Boltzmann Generators -- Sampling Equilibrium States of Many-Body Systems with Deep Learning](https://mlsanity.com/paper/1812.01729/) (2018)
- [Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation](https://mlsanity.com/paper/2410.20255/) (2024)

## Abstract (arXiv)

Generating molecular dynamics (MD) trajectories using deep generative models has attracted increasing attention, yet remains inherently challenging due to the limited availability of MD data and the complexities involved in modeling high-dimensional MD distributions. To overcome these challenges, we propose a novel framework that leverages structure pretraining for MD trajectory generation. Specifically, we first train a diffusion-based structure generation model on a large-scale conformer dataset, on top of which we introduce an interpolator module trained on MD trajectory data, designed to enforce temporal consistency among generated structures. Our approach effectively harnesses abundant structural data to mitigate the scarcity of MD trajectory data and effectively decomposes the intricate MD modeling task into two manageable subproblems: structural generation and temporal alignment. We comprehensively evaluate our method on the QM9 and DRUGS small-molecule datasets across unconditional generation, forward simulation, and interpolation tasks, and further extend our framework and analysis to tetrapeptide and protein monomer systems. Experimental results confirm that our approach excels in generating chemically realistic MD trajectories, as evidenced by remarkable improvements of accuracy in geometric, dynamical, and energetic measurements.