Memory-Efficient Implementation of a Rigid-Body Molecular Dynamics Simulation
Wolfgang Eckhardt, Tobias Neckel · 2012
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.