Memory-Efficient Implementation of a Rigid-Body Molecular Dynamics Simulation

Abstract

Molecular dynamics simulations are usually optimized with regard to runtime rather than memory consumption. In this paper, we investigate two distinct implementational aspects of the frequently used Linked-Cell algorithm for rigid-body molecular dynamics simulations: the representation of particle data for the force calculation, and the layout of data structures in memory. We propose a low memory footprint implementation, which comes with no costs in terms of runtime. To prove the approach, it was implemented in the programme Mardyn and evaluated on a standard cluster as well as on a Blue Gene/P for representative scenarios.