2008/06/24 by David E. Shaw, Martin M. Deneroff, Ron O. Dror +24 · 1 citation
Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · #Protein Structure and Dynamics #Advanced NMR Techniques and Applications #Parallel Computing and Optimization Techniques #Millisecond #Computer science #Massively parallel #Flexibility (engineering) #Range (aeronautics) #Molecular dynamics #Parallel computing #Computational science #Parallelism (grammar) #Physics
paper · pdf · doi:10.1145/1364782.1364802
openalex publication_date 2008/06/24 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/16
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 interact in a tightly coupled manner using a specialized highspeed 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.