A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations

Cell lists are ubiquitous in molecular dynamics simulations—be it for the direct computation of short-range inter-atomic potentials, the short-range direct part of a long-range interaction or for the periodic construction of Verlet lists. The conventional approach to computing pairwise interactions using cell lists leads to a large number of unnecessary interparticle distance calculations. In this paper, an algorithm is presented which reduces the number of spurious distance calculations by first sorting the particles along the cell pair axis and then only interacting two particles if their distance along the axis is smaller than the cutoff distance of the interaction. This approach is shown to be more efficient than the conventional approach and similar approaches using smaller cells. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 570–573, 2007