NEMAT: An Automated Non-Equilibrium Free-Energy Framework for Predicting Ligand Affinity in Membrane Proteins

NEMAT (Non-Equilibrium Membrane Alchemical Transformations) is an open-source framework designed to make non-equilibrium free-energy calculations for ligand binding in membrane proteins accessible, reproducible, and automated.

Built around established molecular simulation workflows, NEMAT guides users through the full process—from system preparation and execution to analysis—enabling the estimation of ligand binding affinities directly from non-equilibrium molecular dynamics simulations. It is particularly tailored for membrane protein systems, where setup and analysis are often complex and error-prone.

By providing a structured, modular workflow, NEMAT reduces manual intervention, improves consistency across simulations, and allows researchers to focus on interpreting results rather than managing infrastructure.

For detailed instructions on execution, configuration, available options, and tutorials, please refer to the project documentation.