NDLI: Anton, a special-purpose machine for molecular dynamics simulation

Content Provider	ACM Digital Library
Author	Wang, Stanley C. Kuskin, Jeffrey S. Shan, Yibing Towles, Brian Shaw, David E. Mueller, Rolf Dror, Ron O. Larson, Richard H. Salmon, John K. Eastwood, Michael P. Grossman, J. P. Layman, Timothy Ho, C. Richard Deneroff, Martin M. Gagliardo, Joseph Spengler, Jochen Ierardi, Douglas J. Moraes, Mark A. Young, Cliff Chao, Jack C. Kolossváry, István Batson, Brannon Bowers, Kevin J. McLeavey, Christine Theobald, Michael Klepeis, John L. Priest, Edward C.
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.
Starting Page	1
Ending Page	12
Page Count	12
File Format	PDF
ISSN	01635964
DOI	10.1145/1273440.1250664
Journal	ACM SIGARCH Computer Architecture News (CARN)
Volume Number	35
Issue Number	2
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	1981-04-01
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Protein folding Biomolecular system simulation Special-purpose machine Molecular dynamics Computational drug design Bioinformatics Protein structure Computational biology
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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