title: Accelerating molecular dynamic simulation on graphics processing units.
abstract: We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core.
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California 94305, USA.
authors.forename: Mark S
authors.initials: MS
authors.lastname: Friedrichs
authors.forename: Peter
authors.initials: P
authors.lastname: Eastman
authors.forename: Vishal
authors.initials: V
authors.lastname: Vaidyanathan
authors.forename: Mike
authors.initials: M
authors.lastname: Houston
authors.forename: Scott
authors.initials: S
authors.lastname: Legrand
authors.forename: Adam L
authors.initials: AL
authors.lastname: Beberg
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Ensign
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Bruns
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000191:economics / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation / Q000191:economics*; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013997:Time Factors
chemical_list: D011506:Proteins; D012997:Solvents