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

revised on 16.02.2021, 04:57 and posted on 16.02.2021, 07:53 by Yunhui Ge, David F. Hahn, David Mobley

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.


Computational alchemy for molecular design and optimization

National Institute of General Medical Sciences

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Open Data-driven Infrastructure for Building Biomolecular Force Field for Predictive Biophysics and Drug Design

National Institute of General Medical Sciences

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Email Address of Submitting Author


University of California, Irvine


United States

ORCID For Submitting Author


Declaration of Conflict of Interest

DLM is a member of the Scientific Advisory Board of OpenEye Scientific Software and an Open Science Fellow with Silicon Therapeutics.

Version Notes

version v2