Microsecond Simulation in a Special-Purpose Molecular Dynamics Computer Cluster

The ability to perform microseconds simulations of molecular dynamics (MD) involving proteins and other biological macromolecules could allow scientists and drug designers to visualize many critically important biochemical phenomena at an atomic level of details that cannot currently be observed in laboratory experiments. However, it will take several months to perform these simulations on a commodity computer. In this paper, we describe a massively parallel computer cluster, which should be capable of executing microseconds MD simulation of biomolecular systems containing millions of atoms. This high-performance computing (HPC) cluster is designed from the ground up based on configurable chips (Field Programmable Gate Array, FPGAs) to best exploit the capabilities offered by new technologies. We also present the main architectural and algorithmic developments that could achieve 20 times the MD performance of GPU accelerated computers.