静电方法在相对结合自由能计算中的性能基准。
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations.
机构信息
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States.
Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium.
出版信息
J Chem Inf Model. 2021 Mar 22;61(3):1048-1052. doi: 10.1021/acs.jcim.0c01424. Epub 2021 Mar 9.
Abstract
Relative free energy calculations are fast becoming a critical part of early stage pharmaceutical design, making it important to know how to obtain the best performance with these calculations in applications that 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 nonequilibrium switching protocol. We found simulations using RF achieve comparable results to 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.
摘要
相对自由能计算正迅速成为药物设计早期阶段的一个关键部分，因此了解如何在可能涵盖数百个计算和分子的应用程序中获得这些计算的最佳性能非常重要。在这项工作中，我们使用非平衡切换方案比较了相对结合自由能计算中两种不同的长程静电处理方法，即粒子网格 Ewald（PME）和反应场（RF）。我们发现，使用 RF 的模拟可以获得与使用 PME 相当的结果，但在使用 CPU 时效率更高，使用 GPU 时性能相似。这项工作的结果鼓励在分子模拟中更多地使用 RF。
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