title: GPU-accelerated molecular mechanics computations.
abstract: 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. © 2013 Wiley Periodicals, Inc.
authors.affiliation: School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, United Kingdom; School of Computer Science, Cardiff University, Cardiff, CF24 3AA, United Kingdom.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Anthopoulos
authors.forename: Ian
authors.initials: I
authors.lastname: Grimstead
authors.forename: Andrea
authors.initials: A
authors.lastname: Brancale
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D056004:Molecular Dynamics Simulation; D012984:Software; D055672:Static Electricity
keywords: Cuda; GPU; MMFF94; cell lists; molecular mechanics