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Anton, a special-purpose machine for molecular dynamics simulation

Publication ,  Conference
Shaw, DE; Deneroff, MM; Dror, RO; Kuskin, JS; Larson, RH; Salmon, JK; Young, C; Batson, B; Bowers, KJ; Chao, JC; Eastwood, MP; Gagliardo, J ...
Published in: Proceedings - International Symposium on Computer Architecture
October 22, 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. Copyright 2007 ACM.

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Published In

Proceedings - International Symposium on Computer Architecture

DOI

ISSN

1063-6897

Publication Date

October 22, 2007

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1 / 12
 

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Shaw, D. E., Deneroff, M. M., Dror, R. O., Kuskin, J. S., Larson, R. H., Salmon, J. K., … Wang, S. C. (2007). Anton, a special-purpose machine for molecular dynamics simulation. In Proceedings - International Symposium on Computer Architecture (pp. 1–12). https://doi.org/10.1145/1250662.1250664
Shaw, D. E., M. M. Deneroff, R. O. Dror, J. S. Kuskin, R. H. Larson, J. K. Salmon, C. Young, et al. “Anton, a special-purpose machine for molecular dynamics simulation.” In Proceedings - International Symposium on Computer Architecture, 1–12, 2007. https://doi.org/10.1145/1250662.1250664.
Shaw DE, Deneroff MM, Dror RO, Kuskin JS, Larson RH, Salmon JK, et al. Anton, a special-purpose machine for molecular dynamics simulation. In: Proceedings - International Symposium on Computer Architecture. 2007. p. 1–12.
Shaw, D. E., et al. “Anton, a special-purpose machine for molecular dynamics simulation.” Proceedings - International Symposium on Computer Architecture, 2007, pp. 1–12. Scopus, doi:10.1145/1250662.1250664.
Shaw DE, Deneroff MM, Dror RO, Kuskin JS, Larson RH, Salmon JK, Young C, Batson B, Bowers KJ, Chao JC, Eastwood MP, Gagliardo J, Grossman JP, Ho CR, Ierardi DJ, Kolossváry I, Klepeis JL, Layman T, McLeavey C, Moraes MA, Mueller R, Priest EC, Shan Y, Spengler J, Theobald M, Towles B, Wang SC. Anton, a special-purpose machine for molecular dynamics simulation. Proceedings - International Symposium on Computer Architecture. 2007. p. 1–12.

Published In

Proceedings - International Symposium on Computer Architecture

DOI

ISSN

1063-6897

Publication Date

October 22, 2007

Start / End Page

1 / 12