Anton: A Special-Purpose Machine That Achieves a Hundred-Fold Speedup in Biomolecular Simulations

Speaker

David E. Shaw

Abstract

Molecular dynamics (MD) simulation has long been recognized as a potentially transformative tool for understanding the behavior of proteins and other biological macromolecules, and for developing a new generation of precisely targeted drugs. Many biologically important phenomena, however, occur over timescales that have previously fallen far outside the reach of MD technology. We have constructed a specialized, massively parallel machine, called Anton, that is capable of performing atomic-level simulations of proteins at a speed roughly two orders of magnitude beyond that of the previous state of the art. The machine has now simulated the behavior of a number of proteins for periods as long as two milliseconds -- approximately 200 times the length of the longest such simulation previously published. Such simulations have allowed us to elucidate for the first time key aspects of protein dynamics that were previously inaccessible to both computational and experimental study, including some of the most important and longstanding open questions regarding the process of "protein folding." The speed at which Anton performs such simulations is in large part the result of a codesign process in which the machine architecture was developed in concert with novel algorithms, including a highly efficient parallel algorithm for the range-limited N-body problem.