# Generative Modeling of Molecular Dynamics Trajectories

arXiv: https://arxiv.org/abs/2409.17808 · HTML: https://mlsanity.com/paper/2409.17808/

## Key facts

- Cited by 51 papers in the map (data through 14 Oct 2026).
- Builds on 27 of its 53 references that are in the map.
- First posted on arXiv 26 Sep 2024.

## Builds on (most cited first, 27 of 27)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Scaling Rectified Flow Transformers for High-Resolution Image Synthesis](https://mlsanity.com/paper/2403.03206/) (2024)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Video Diffusion Models](https://mlsanity.com/paper/2204.03458/) (2022)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Building Normalizing Flows with Stochastic Interpolants](https://mlsanity.com/paper/2209.15571/) (2022)
- [Stochastic Interpolants: A Unifying Framework for Flows and Diffusions](https://mlsanity.com/paper/2303.08797/) (2023)
- [SiT: Exploring Flow and Diffusion-based Generative Models with Scalable Interpolant Transformers](https://mlsanity.com/paper/2401.08740/) (2024)
- [A Continuous Time Framework for Discrete Denoising Models](https://mlsanity.com/paper/2205.14987/) (2022)
- [Hyena Hierarchy: Towards Larger Convolutional Language Models](https://mlsanity.com/paper/2302.10866/) (2023)
- [Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design](https://mlsanity.com/paper/2402.04997/) (2024)
- [SE(3) diffusion model with application to protein backbone generation](https://mlsanity.com/paper/2302.02277/) (2023)
- [Autoregressive Diffusion Models](https://mlsanity.com/paper/2110.02037/) (2021)
- [E(n) Equivariant Normalizing Flows](https://mlsanity.com/paper/2105.09016/) (2021)
- [Flow Annealed Importance Sampling Bootstrap](https://mlsanity.com/paper/2208.01893/) (2022)
- [Dirichlet Flow Matching with Applications to DNA Sequence Design](https://mlsanity.com/paper/2402.05841/) (2024)
- [AlphaFold Meets Flow Matching for Generating Protein Ensembles](https://mlsanity.com/paper/2402.04845/) (2024)
- [Video as the New Language for Real-World Decision Making](https://mlsanity.com/paper/2402.17139/) (2024)
- [Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics](https://mlsanity.com/paper/2302.01170/) (2023)
- [Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds](https://mlsanity.com/paper/2301.12485/) (2023)
- [Smooth Normalizing Flows](https://mlsanity.com/paper/2110.00351/) (2021)
- [Efficient Video Diffusion Models via Content-Frame Motion-Latent Decomposition](https://mlsanity.com/paper/2403.14148/) (2024)
- [SE(3) Equivariant Augmented Coupling Flows](https://mlsanity.com/paper/2308.10364/) (2023)
- [Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning](https://mlsanity.com/paper/2306.05445/) (2023)
- [Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-Scale Graph Networks](https://mlsanity.com/paper/2204.10348/) (2022)

## Built on by (most cited first, 30 of 51)

- [Scalable Equilibrium Sampling with Sequential Boltzmann Generators](https://mlsanity.com/paper/2502.18462/) (2025)
- [Erwin: A Tree-based Hierarchical Transformer for Large-scale Physical Systems](https://mlsanity.com/paper/2502.17019/) (2025)
- [Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functional](https://mlsanity.com/paper/2504.18506/) (2025)
- [Structure Language Models for Protein Conformation Generation](https://mlsanity.com/paper/2410.18403/) (2024)
- [EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants](https://mlsanity.com/paper/2410.09667/) (2024)
- [SimpleFold: Folding Proteins is Simpler than You Think](https://mlsanity.com/paper/2509.18480/) (2025)
- [Force-Free Molecular Dynamics Through Autoregressive Equivariant Networks](https://mlsanity.com/paper/2503.23794/) (2025)
- [Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models](https://mlsanity.com/paper/2602.16634/) (2026)
- [Amortized Sampling with Transferable Normalizing Flows](https://mlsanity.com/paper/2508.18175/) (2025)
- [Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamics](https://mlsanity.com/paper/2510.07589/) (2025)
- [ConfRover: Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression](https://mlsanity.com/paper/2505.17478/) (2025)
- [Virtual Cells: Predict, Explain, Discover](https://mlsanity.com/paper/2505.14613/) (2025)
- [UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules](https://mlsanity.com/paper/2506.03157/) (2025)
- [Accelerating Protein Molecular Dynamics Simulation with DeepJump](https://mlsanity.com/paper/2509.13294/) (2025)
- [MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models](https://mlsanity.com/paper/2509.24779/) (2025)
- [Aligning Protein Conformation Ensemble Generation with Physical Feedback](https://mlsanity.com/paper/2505.24203/) (2025)
- [HollowFlow: Efficient Sample Likelihood Evaluation using Hollow Message Passing](https://mlsanity.com/paper/2510.21542/) (2025)
- [A Definition and Roadmap for World Models](https://mlsanity.com/paper/2607.06401/) (2026)
- [JAMUN: Bridging Smoothed Molecular Dynamics and Score-Based Learning for Conformational Ensembles](https://mlsanity.com/paper/2410.14621/) (2024)
- [Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics](https://mlsanity.com/paper/2602.02128/) (2026)
- [Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators](https://mlsanity.com/paper/2602.11216/) (2026)
- [Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems](https://mlsanity.com/paper/2508.12569/) (2025)
- [Beyond Ensembles: Simulating All-Atom Protein Dynamics in a Learned Latent Space](https://mlsanity.com/paper/2509.02196/) (2025)
- [TEMPO: Temporal Multi-scale Autoregressive Generation of Protein Conformational Ensembles](https://mlsanity.com/paper/2511.05510/) (2025)
- [World Models as Group Actions](https://mlsanity.com/paper/2605.24578/) (2026)
- [Template-Guided 3D Molecular Pose Generation via Flow Matching and Differentiable Optimization](https://mlsanity.com/paper/2506.06305/) (2025)
- [Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings](https://mlsanity.com/paper/2506.17064/) (2025)
- [Accelerating Long-Term Molecular Dynamics with Physics-Informed Time-Series Forecasting](https://mlsanity.com/paper/2510.01206/) (2025)
- [Unified Biomolecular Trajectory Generation via Pretrained Variational Bridge](https://mlsanity.com/paper/2602.07588/) (2026)
- [Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics](https://mlsanity.com/paper/2603.17633/) (2026)

## Abstract (arXiv)

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.