An Algorithm for Computing Short-Range Forces in Molecular Dynamics Simulations with Non-Uniform Particle Densities

We present projection sorting, an algorithmic approach to determining pairwise short-range forces between particles in molecular dynamics simulations. We show it can be more effective than the standard approaches when particle density is non-uniform. We implement tuned versions of the algorithm in the context of a biophysical simulation of chromosome condensation, for the modern Intel Broadwell and Knights Landing architectures, across multiple nodes. We demonstrate up to 5x overall speedup and good scaling to large problem sizes and processor counts.