Molecular dynamics (MD) simulations offer a tantalizing window into the workings of biological systems in full atomistic detail. The promise of this methodology for obtaining detailed understanding of biomolecular mechanisms depends in part on the ability of these simulations to reach biologically-relevant timescales. Due to the tremendous gap between the timescales of atomistic motion and the timescales of biological processes, simulation of these processes requires extremely efficient parallel implementations of MD algorithms on high performance computing systems. Recent implementations of MD algorithms on specialized hardware are poised to significantly increase our ability to study biological processes, as well as vigorously test the accuracy of these methods. In this talk I will discuss, in the context of these recent developments, some of my work to facilitate the study of biological processes through molecular dynamics simulations.