Anton, a special-purpose machine for molecular dynamics simulation

• Authors: David E. Shaw;Martin M. Deneroff;Ron O. Dror;Jeffrey S. Kuskin;Richard H. Larson;John K. Salmon;Cliff Young;Brannon Batson;Kevin J. Bowers;Jack C. Chao;Michael P. Eastwood;Joseph Gagliardo;J. P. Grossman;C. Richard Ho;Douglas J. Ierardi;István Kolossváry;John L. Klepeis;Timothy Layman;Christine McLeavey;Mark A. Moraes;Rolf Mueller;Edward C. Priest;Yibing Shan;Jochen Spengler;Michael Theobald;Brian Towles;Stanley C. Wang
• Venue: Proceedings of the 34th annual international symposium on Computer architecture
• Year: 2007

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 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.