Journal Of Computational Chemistry [J Comput Chem] 2010 Apr 30; Vol. 31 (6), pp. 1268-72.
Algorithms, Lipid Bilayers chemistry, Molecular Dynamics Simulation, and Proteins chemistry
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. (2009 Wiley Periodicals, Inc.)