GitHub

Publications

Citation

If you use Molly, please cite the following paper (bib entry here):

  • Greener JG. Differentiable simulation to develop molecular dynamics force fields for disordered proteins, Chemical Science 15, 4897-4909 (2024)

A paper involving more contributors with further details on the software will be written at some point.

Relevant papers

Other papers that use, contribute to or are compatible with Molly are listed below:

  • Martínez L. CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties within a cutoff, Comput Phys Commun 279, 108452 (2022)
  • Witt WC et al. ACEpotentials.jl: A Julia implementation of the atomic cluster expansion, J Chem Phys 159, 164101 (2023)
  • Blassel N and Stoltz G. Fixing the Flux: A Dual Approach to Computing Transport Coefficients, Journal of Statistical Physics 191, 17 (2024)
  • Spacek R, Monmarché P and Stoltz G. Transient Subtraction: A Control Variate Method for Computing Transport Coefficients, Journal of Statistical Physics 192, 53 (2025)
  • Wu X, Shang X. Stochastic Norton Dynamics: An Alternative Approach for the Computation of Transport Coefficients in Dissipative Particle Dynamics, arXiv (2025)
  • Greener JG. Reversible molecular simulation for training classical and machine learning force field, Proceedings of the National Academy of Sciences 122(22), e2426058122 (2025)
  • Blanco-González A, Schulze TK, Rovers E, Greener JG. Training a force field for proteins and small molecules from scratch, arXiv (2026)

General resources

Some general resources for learning molecular dynamics include:

Papers relevant to particular functions and structs are referenced in the docstrings. See the documentation home page for some talk recordings and slides about Molly.