Paper Citing NAMD - Abstract
Shaw, David E.; Deneroff, Martin M.; Dror, Ron O.; Kuskin, Jeffrey S.; Larson, Richard H.; Salmon, John K.; Young, Cliff; Batson, Brannon; Bowers, Kevin J.; Chao, Jack C.; Eastwood, Michael P.; Gagliardo, Joseph; Grossman, J. P.; Ho, C. Richard; Ierardi, Douglas J.; Kolossvary, Istvan; Klepeis, John L.; Layman, Timothy; Mcleavey, Christine; Moraes, Mark A.; Mueller, Rolf; Priest, Edward C.; Shan, Yibing; Spengler, Jochen; Theobald, Michael; Towles, Brian; Wang, Stanley C.
Anton, a special-purpose machine for molecular dynamics simulation
COMMUNICATIONS OF THE ACM, 51:91-97, JUL 2008
The ability to perform long, accurate molecular dynamics ( MD) simulations involving proteins and other biological macromolecules 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.
