A Benchmark of Electrostatic Methods Performance in Relative Binding Free Energy Calculations

Relative free energy calculations are fast becoming a critical part of early stage pharmaceu- tical design, making it important to know how to obtain the best performance with these calculations in applications which could span hundreds of calculations and molecules. In this work, we compared two different treatments of long-range electrostatics, Particle Mesh Ewald (PME) and Reaction Field (RF), in relative binding free energy calculations using a non-equilibrium switching protocol. We found simulations using RF achieve comparable re- sults as those using PME but gain more efficiency when using CPU and similar performance using GPU. The results from this work encourage more use of RF in molecular simulations.