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Efficient nonbonded interactions for molecular dynamics on a graphics processing unit
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
doi:10.1002/jcc.21413
pmid:19847780
pmcid:PMC2841709
fatcat:ksunpvpdxfadnmr2xzcvfjyj4e