Anton, a special-purpose machine for molecular dynamics simulation

ABSTRACT

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.

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INDEX TERMS

Primary Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

Additional Classification:
  C. Computer Systems Organization
  C.1 PROCESSOR ARCHITECTURES
      C.1.4 Parallel Architectures
  C.3 SPECIAL-PURPOSE AND APPLICATION-BASED SYSTEMS
      Subjects: Microprocessor/microcomputer applications

  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Health

General Terms:
Algorithms, Design, Performance

Keywords:
bioinformatics, biomolecular system simulation, computational biology, computational drug design, molecular dynamics, protein folding, protein structure, special-purpose machine