Paper Citing NAMD - Abstract
Gonnet, Pedro
Pairwise Verlet Lists: Combining Cell Lists and Verlet Lists to Improve Memory Locality and Parallelism
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:76-81, JAN 5 2012
Verlet lists, which are commonly used in many particle-based simulations, are not suited for modern, shared-memory parallel multicore architectures. In this article, we introduce pairwise Verlet lists: local Verlet lists containing only interacting particle pairs between a pair of neighboring computational cells. We show that these pairwise Verlet lists are more efficient and scale much better than the traditional global Verlet list, both on a single processor as well as on multiple shared-memory cores. The improved performance on a single core makes them an interesting option for distributed-memory simulations as well. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 33: 76-81, 2012
