Architectures and Algorithms for

Millisecond-Scale Molecular Dynamics Simulations of Proteins

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle lead to important scientific advances and provide a powerful new tool for drug discovery. A wide range of biologically interesting phenomena, however, occur over time scales on the order of a millisecond -- about three orders of magnitude beyond the duration of the longest current MD simulations. Our research group is currently building a specialized, massively parallel machine called Anton which, when completed in late 2008, should be capable of executing millisecond-scale classical MD simulations of one or more proteins at an atomic level of detail. We have also recently completed a parallel MD package called Desmond, which uses novel algorithms to achieve unprecedented simulation speed on an ordinary computational cluster. This talk will provide an overview of our work on parallel algorithms and machine architectures for high-speed MD simulation, and will describe research conducted recently within our lab in which lengthy Desmond simulations helped elucidate the dynamics and functional mechanisms of two biologically important proteins. These computational studies yielded testable predictions which have subsequently been validated through laboratory experiments.