Publications

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.

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)