Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

Peter Eastman, Vijay S. Pande
2009 Journal of Computational Chemistry  
We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit (GPU). 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
more » ... ge of system sizes, while being significantly faster than other published algorithms.
doi:10.1002/jcc.21413 pmid:19847780 pmcid:PMC2841709 fatcat:ksunpvpdxfadnmr2xzcvfjyj4e