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

preprint
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.

Funding

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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History

Email Address of Submitting Author

yunhui.ge@gmail.com

Institution

University of California, Irvine

Country

United States

ORCID For Submitting Author

0000-0002-3946-1440

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

Exports