Input files for the simulation were adapted from https://github.com/linfranksong/Input_TI, and can be found here: https://github.com/openmm/openmmforcefields/tree/master/openmmforcefields/data/perses_jacs_systems
Using openmm-forcefields: - amber/protein.ff14SB.xml - amber/tip3p_standard.xml - amber/tip3p_HFE_multivalent.xml
Several different small molecule forcefields have been used, and results are in folders named accordingly.
Wang, L., Wu, Y., Deng, Y., Kim, B., Pierce, L., Krilov, G., ... & Romero, D. L. (2015). Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. Journal of the American Chemical Society, 137(7), 2695-2703.