The DOI matches its Crossref record; 22 of the 22 references it cites were found in a registry or an index.
Anton, a special-purpose machine for molecular dynamics simulation
Open accessAbstract
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.
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Cited by
Molecular Dynamics Simulation for All
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Metadata
- Authors
- Shaw, D. E., Deneroff, M. M., Dror, R. O., Kuskin, J. S., Larson, R. H., Salmon, J. K., Young, C., Batson, B., Bowers, K. J., Chao, J. C., Eastwood, M. P., Gagliardo, J., Grossman, J. P., Ho, C. R., Ierardi, D. J., Kolossváry, I., Klepeis, J. L., Layman, T., McLeavey, C., Moraes, M. A., Mueller, R., Priest, E. C., Shan, Y., Spengler, J., Theobald, M., Towles, B., & Wang, S. C.
- Venue
- Communications of the ACM
- Published
- 2008-07
- Volume
- 51
- Issue
- 7
- Pages
- 91-97
- ISSN
- 0001-0782 (ISSN-L)
- 1557-7317
- OpenAlex
- W2028263411
- Cited by
- 817
- References
- 22
- FWCI
- 54.51
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Shaw, D. E., Deneroff, M. M., Dror, R. O., Kuskin, J. S., Larson, R. H., Salmon, J. K., Young, C., Batson, B., Bowers, K. J., Chao, J. C., Eastwood, M. P., Gagliardo, J., Grossman, J. P., Ho, C. R., Ierardi, D. J., Kolossváry, I., Klepeis, J. L., Layman, T., McLeavey, C., . . . Wang, S. C. (2008). Anton, a special-purpose machine for molecular dynamics simulation. Communications of the ACM. https://doi.org/10.1145/1364782.1364802
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