Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.
We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit. We have incorporated it into OpenMM, a library for performing molecular simulations on high-performance computer architectures. We benchmark it on a variety of systems including boxes of water molecules, proteins in explicit solvent, a lipid bilayer, and proteins with implicit solvent. The results demonstrate that its performance scales linearly with the number of atoms over a wide range of system sizes, while being significantly faster than other published algorithms.
Eastman
Peter
P
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. peastman@stanford.edu
Pande
Vijay S
VS
D000465:Algorithms; D008051:Lipid Bilayers / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*
D008051:Lipid Bilayers; D011506:Proteins