# Machine Learning of coarse-grained Molecular Dynamics Force Fields

arXiv: https://arxiv.org/abs/1812.01736 · HTML: https://mlsanity.com/paper/1812.01736/

## Key facts

- Cited by 69 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 4 Dec 2018.

## Built on by (most cited first, 30 of 69)

- [TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials](https://mlsanity.com/paper/2202.02541/) (2022)
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- [Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations](https://mlsanity.com/paper/2210.07237/) (2022)
- [Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics](https://mlsanity.com/paper/2302.00600/) (2023)
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- [Physics-Guided Deep Learning for Dynamical Systems: A Survey](https://mlsanity.com/paper/2107.01272/) (2021)
- [Machine Learning Coarse-Grained Potentials of Protein Thermodynamics](https://mlsanity.com/paper/2212.07492/) (2022)
- [Flow-matching -- efficient coarse-graining of molecular dynamics without forces](https://mlsanity.com/paper/2203.11167/) (2022)
- [Graph Neural Networks Accelerated Molecular Dynamics](https://mlsanity.com/paper/2112.03383/) (2021)
- [Constructing Neural Network-Based Models for Simulating Dynamical Systems](https://mlsanity.com/paper/2111.01495/) (2021)
- [Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling](https://mlsanity.com/paper/2306.03117/) (2023)
- [Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting](https://mlsanity.com/paper/2106.01138/) (2021)
- [Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning](https://mlsanity.com/paper/2306.05445/) (2023)
- [The dark side of the forces: assessing non-conservative force models for atomistic machine learning](https://mlsanity.com/paper/2412.11569/) (2024)
- [Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-Scale Graph Networks](https://mlsanity.com/paper/2204.10348/) (2022)
- [Navigating protein landscapes with a machine-learned transferable coarse-grained model](https://mlsanity.com/paper/2310.18278/) (2023)
- [PET-MAD, a lightweight universal interatomic potential for advanced materials modeling](https://mlsanity.com/paper/2503.14118/) (2025)
- [Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models](https://mlsanity.com/paper/2506.17139/) (2025)
- [Generative Coarse-Graining of Molecular Conformations](https://mlsanity.com/paper/2201.12176/) (2022)
- [Score dynamics: scaling molecular dynamics with picoseconds timestep via conditional diffusion model](https://mlsanity.com/paper/2310.01678/) (2023)
- [EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants](https://mlsanity.com/paper/2410.09667/) (2024)
- [Implicit Transfer Operator Learning: Multiple Time-Resolution Surrogates for Molecular Dynamics](https://mlsanity.com/paper/2305.18046/) (2023)
- [Towards equilibrium molecular conformation generation with GFlowNets](https://mlsanity.com/paper/2310.14782/) (2023)
- [Overcoming the Barrier of Orbital-Free Density Functional Theory for Molecular Systems Using Deep Learning](https://mlsanity.com/paper/2309.16578/) (2023)
- [Neural Markov Jump Processes](https://mlsanity.com/paper/2305.19744/) (2023)
- [chemtrain: Learning Deep Potential Models via Automatic Differentiation and Statistical Physics](https://mlsanity.com/paper/2408.15852/) (2024)
- [Scalable Bayesian Uncertainty Quantification for Neural Network Potentials: Promise and Pitfalls](https://mlsanity.com/paper/2212.07959/) (2022)
- [Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamics](https://mlsanity.com/paper/2510.07589/) (2025)
- [DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces](https://mlsanity.com/paper/2307.12451/) (2023)

## Abstract (arXiv)

Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such computationally expensive simulations is the definition of coarse-grained molecular models. Existing coarse-graining approaches define an effective interaction potential to match defined properties of high-resolution models or experimental data. In this paper, we reformulate coarse-graining as a supervised machine learning problem. We use statistical learning theory to decompose the coarse-graining error and cross-validation to select and compare the performance of different models. We introduce CGnets, a deep learning approach, that learns coarse-grained free energy functions and can be trained by a force matching scheme. CGnets maintain all physically relevant invariances and allow one to incorporate prior physics knowledge to avoid sampling of unphysical structures. We show that CGnets can capture all-atom explicit-solvent free energy surfaces with models using only a few coarse-grained beads and no solvent, while classical coarse-graining methods fail to capture crucial features of the free energy surface. Thus, CGnets are able to capture multi-body terms that emerge from the dimensionality reduction.