title: Interaction sorting method for molecular dynamics on multi-core SIMD CPU architecture.
abstract: Molecular dynamics (MD) is widely used in computational biology for studying binding mechanisms of molecules, molecular transport, conformational transitions, protein folding, etc. The method is computationally expensive; thus, the demand for the development of novel, much more efficient algorithms is still high. Therefore, the new algorithm designed in 2007 and called interaction sorting (IS) clearly attracted interest, as it outperformed the most efficient MD algorithms. In this work, a new IS modification is proposed which allows the algorithm to utilize SIMD processor instructions. This paper shows that the improvement provides an additional gain in performance, 9% to 45% in comparison to the original IS method.
authors.affiliation: Nosovibirsk State University, 2 Pirogova Str, Novosibirsk 630090, Russian Federation.
authors.forename: Sergey
authors.initials: S
authors.lastname: Matvienko
authors.forename: Nikolay
authors.initials: N
authors.lastname: Alemasov
authors.forename: Eduard
authors.initials: E
authors.lastname: Fomin
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D056004:Molecular Dynamics Simulation
keywords: Molecular dynamics; SIMD; cell linked list; interaction sort; neighbour search