Paper Citing NAMD - Abstract
Gonnet, Pedro
Pseudo-Verlet lists: a new, compact neighbour list representation
MOLECULAR SIMULATION, 39:721-727, AUG 1 2013
Verlet lists, or neighbour lists, are a popular device to speed up the computation of non-bonded interactions in molecular dynamics and other particle-based simulations, in which a list of interacting particles for a given geometry is computed once and reused over several time steps until the geometry changes significantly. The size of the Verlet list is generally indices in the range , where N is the total number of particles, (N) is the particle number density and r(c) and r(s) are the cutoff and skin distances, respectively. Due to their memory requirements, Verlet lists are not always an optimal choice on multi-core or graphics processing unit systems in which the memory bandwidth per core is limited. This paper introduces pseudo-Verlet lists, an alternative neighbour list representation which requires only 13N indices in the range , thus requiring less storage, and resulting in better cache reuse.
