title: Computation of induced dipoles in molecular mechanics simulations using graphics processors.
abstract: In this work, we present a tentative step toward the efficient implementation of polarizable molecular mechanics force fields with GPU acceleration. The computational bottleneck of such applications is found in the treatment of electrostatics, where higher-order multipoles and a self-consistent treatment of polarization effects are needed. We have implemented a GPU accelerated code, based on the Tinker program suite, for the computation of induced dipoles. The largest test system used shows a speedup factor of over 20 for a single precision GPU implementation, when comparing to the serial CPU version. A discussion of the optimization and parametrization steps is included. Comparison between different graphic cards and CPU-GPU embedding is also given. The current work demonstrates the potential usefulness of GPU programming in accelerating this field of applications.
authors.affiliation: INESC-ID/IST, Technical University of Lisbon , Rua Alves Redol 9, 1000-029 Lisboa, Portugal.
authors.forename: Frederico
authors.initials: F
authors.lastname: Pratas
authors.forename: Leonel
authors.initials: L
authors.lastname: Sousa
authors.forename: Johannes M
authors.initials: JM
authors.lastname: Dieterich
authors.forename: Ricardo A
authors.initials: RA
authors.lastname: Mata
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D025801:Ubiquitin / Q000737:chemistry; D014867:Water / Q000737:chemistry
chemical_list: D025801:Ubiquitin; D014867:Water