Software

FastMBAR is a Python solver for large scale MBAR/UWHAM equations running on both CPUs and GPUs. It can compute relative free energies of a large number of thermodynamic states used in alchemical free energy calculations and calculating potential of mean force (PMF) in umbrella sampling and temperature/Hamiltonian replica exchange simulations.

Potential contrasting is an efficient method for learning a potential energy function that can reproduce an ensemble of molecular conformations. It can be easily applied to can learn coarse-grained force fields based on all-atom simulations. It generalizes the noise contrastive esitmation method to use complex unnormalized noise distributions constructed using molecular dynamics techniques such as umbrella sampling.