Simbios Talk by David Shaw, D. E. Shaw Research and Center for Computational Biology and Bioinformatics, Columbia University, January 14, 2009

Title: Anton: A Specialized Machine for Millisecond-Scale Molecular Dynamics Simulations of Proteins

The ability to perform long, accurate, atomic-level molecular dynamics (MD) simulations of proteins surrounded by explicitly represented water molecules could in principle provide scientifically (and perhaps pharmaceutically) relevant insights into the structural, dynamic, and functional characteristics of proteins. A wide range of biologically significant phenomena, however, occur over timescales on the order of a millisecond—at least two orders of magnitude beyond the reach of the longest previous MD simulations. We have recently constructed a working prototype of the first of 16 “segments” of a specialized, massively parallel machine, called Anton, designed specifically for the execution of MD simulations. Each Anton segment was designed to simulate a single MD trajectory as much as a millisecond or so in length using novel algorithms developed within our lab. The prototype machine very quickly generated the world’s longest (by a significant factor) MD trajectory, and is now being used within our lab for preliminary tests involving the simulation of a number of proteins.

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 within our lab in which simulations of moderate length have helped elucidate the dynamics and functional mechanisms of several biologically important proteins. Some of these computational studies have yielded testable predictions that have subsequently been validated through laboratory experiments.