Anton, a Special-Purpose Machine for Molecular Dynamics Simulation

DE Shaw and MM Deneroff and RO Dror and JS Kuskin and RH Larson and JK Salmon and C Young and B Batson and KJ Bowers and JC Chao and MP Eastwood and J Gagliardo and JP Grossman and CR Ho and DJ Ierardi and I Kolossvary and JL Klepeis and T Layman and C McLeavey and MA Moraes and R Mueller and EC Priest and YB Shan and J Spengler and M Theobald and B Towles and SC Wang, ISCA'07: 34TH ANNUAL INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE, CONFERENCE PROCEEDINGS, 1-12 (2007).

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules 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 time scales on the order of a millisecond-about three orders of magnitude beyond the duration of the longest current MD simulations. In this paper, 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 interact 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 remainder of the simulation algorithm is executed by a programmable portion of each chip that achieves a substantial degree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods.

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