a special purpose machine for molecular dynamics simulation

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry, and medicine. A wide range of biologically interesting phenomena, however, occur over timescales on the order of a millisecond—several orders of magnitude beyond the duration of the longest current MD simulations. We describe a massively parallel machine called Anton, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that in-teract in a tightly coupled manner using a specialized high-speed communication network. Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation. The remain-der of the simulation algorithm is executed by a program-mable portion of each chip that achieves a substantial de-gree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods. 1