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GPU-accelerated molecular mechanics computations

Anthopoulos, Athanasios, Grimstead, Ian John and Brancale, Andrea ORCID: 2013. GPU-accelerated molecular mechanics computations. Journal of Computational Chemistry 34 (26) , pp. 2249-2260. 10.1002/jcc.23384

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In this article, we describe an improved cell-list approach designed to match the Kepler architecture of General-purpose graphics processing units (GPGPU). We explain how our approach improves load balancing for the above algorithm and how warp intrinsics are used to implement Newton's third law for the nonbonded force calculations. We also talk through our approach to exclusions handling together with a method to calculate bonded forces and 1–4 electrostatic scaling using a single Cuda kernel. Performance benchmarks are included in the last sections to show the linear scaling of our implementation using a step minimization method. In addition, multiple performance benchmarks demonstrate the contribution of various optimizations we used for our implementations.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Computer Science & Informatics
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
R Medicine > RS Pharmacy and materia medica
Uncontrolled Keywords: GPU; molecular mechanics; MMFF94; cell lists; Cuda
Publisher: Wiley
ISSN: 0192-8651
Last Modified: 06 Jan 2024 05:12

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