Paper Citing NAMD - Abstract
Eastman, Peter; Pande, Vijay S.
Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:1268-1272, APR 30 2010
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. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 31: 1268-1272, 2010
