Code illustrating the use of belief propagation on factor graphs for molecular simulation. The learned factors may be exported into static bias files for PLUMED. Please read and cite the following manuscript when using this code: https://www.biorxiv.org/content/10.1101/2021.06.28.450193v1.abstract
Module containing all of the classes and functions used to generate a factorized model from an input trajectory.
Example notebook walking through the methods used in the manuscript.
Input trajectory for Ala3 used in the manuscript.
Pickle containing the original factorized model used in the manuscript.
Directory containing all the inputs required for reproducing simulations.