# Molecular Latent Space Simulators

arXiv: https://arxiv.org/abs/2007.00728 · HTML: https://mlsanity.com/paper/2007.00728/

## Key facts

- Cited by 14 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 1 Jul 2020.

## Built on by (most cited first, 14 of 14)

- [Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling](https://mlsanity.com/paper/2410.07974/) (2024)
- [Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-Scale Graph Networks](https://mlsanity.com/paper/2204.10348/) (2022)
- [Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamics](https://mlsanity.com/paper/2510.07589/) (2025)
- [Latent Representation and Simulation of Markov Processes via Time-Lagged Information Bottleneck](https://mlsanity.com/paper/2309.07200/) (2023)
- [Path sampling of recurrent neural networks by incorporating known physics](https://mlsanity.com/paper/2203.00597/) (2022)
- [GANs and Closures: Micro-Macro Consistency in Multiscale Modeling](https://mlsanity.com/paper/2208.10715/) (2022)
- [Micro-Macro Consistency in Multiscale Modeling: Score-Based Model Assisted Sampling of Fast/Slow Dynamical Systems](https://mlsanity.com/paper/2312.05715/) (2023)
- [Beyond Ensembles: Simulating All-Atom Protein Dynamics in a Learned Latent Space](https://mlsanity.com/paper/2509.02196/) (2025)
- [Accelerated Simulations of Molecular Systems through Learning of their Effective Dynamics](https://mlsanity.com/paper/2102.08810/) (2021)
- [Staying the course: Locating equilibria of dynamical systems on Riemannian manifolds defined by point-clouds](https://mlsanity.com/paper/2204.10413/) (2022)
- [AI-based Methods for Simulating, Sampling, and Predicting Protein Ensembles](https://mlsanity.com/paper/2509.17224/) (2025)
- [Consistent Projection of Langevin Dynamics: Preserving Thermodynamics and Kinetics in Coarse-Grained Models](https://mlsanity.com/paper/2512.03706/) (2025)
- [SupraTITO: Transferable Generative Molecular Dynamics for Supramolecular Systems](https://mlsanity.com/paper/2610.01381/) (2026)
- [Looking Under the Streetlight: Evaluation in Generative Molecular Dynamics](https://mlsanity.com/paper/2610.12518/) (2026)

## Abstract (arXiv)

Small integration time steps limit molecular dynamics (MD) simulations to millisecond time scales. Markov state models (MSMs) and equation-free approaches learn low-dimensional kinetic models from MD simulation data by performing configurational or dynamical coarse-graining of the state space. The learned kinetic models enable the efficient generation of dynamical trajectories over vastly longer time scales than are accessible by MD, but the discretization of configurational space and/or absence of a means to reconstruct molecular configurations precludes the generation of continuous all-atom molecular trajectories. We propose latent space simulators (LSS) to learn kinetic models for continuous all-atom simulation trajectories by training three deep learning networks to (i) learn the slow collective variables of the molecular system, (ii) propagate the system dynamics within this slow latent space, and (iii) generatively reconstruct molecular configurations. We demonstrate the approach in an application to Trp-cage miniprotein to produce novel ultra-long synthetic folding trajectories that accurately reproduce all-atom molecular structure, thermodynamics, and kinetics at six orders of magnitude lower cost than MD. The dramatically lower cost of trajectory generation enables greatly improved sampling and greatly reduced statistical uncertainties in estimated thermodynamic averages and kinetic rates.