Accelerating Molecular Dynamic Simulation on Graphics Processing Units

Overview

Journal J Comput Chem

Publisher Wiley

Specialties Biology
Chemistry

Date 2009 Feb 5

PMID 19191337

Citations 163

Authors

Mark S Friedrichs

Peter Eastman

Vishal Vaidyanathan

Mike Houston

Scott LeGrand

Adam L Beberg

Daniel L Ensign

Christopher M Bruns

Vijay S Pande

Affiliations

Soon will be listed here.

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.

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