Paper Info
Title
Architectures and algorithms for millisecond-scale molecular dynamics simulations of proteins
Abstract
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle lead to important scientific advances and provide a powerful new tool for drug discovery. A wide range of biologically interesting phenomena, however, occur over time scales on the order of a millisecond - several orders of magnitude beyond the duration of the longest current MD simulations. Our research group is currently building a specialized, massively parallel machine, called Anton, which should soon be capable of executing millisecond-scale MD simulations of proteins at an atomic level of detail. Anton’s highly accelerated execution of such simulations is attributable in large part to specialized logic for the high-speed calculation of pairwise interactions between particles and/or gridpoints separated by no more than some specified cutoff radius.
Year
DOI
Venue
2008
10.1109/MICRO.2008.4771773
MICRO
Keywords
DocType
Volume
atomic level,millisecond-scale md simulation,longest current md simulation,accelerated execution,high-speed calculation,millisecond-scale molecular dynamics simulation,accurate molecular dynamic,drug discovery,biologically interesting phenomenon,biological macromolecule,specialized logic,pipelines,computational modeling,macromolecules,computer architecture,proteins,high throughput,chip,molecular dynamic,level of detail,parallel algorithm
Conference
237
ISSN
Citations 
PageRank 
0065-7727
0
0.34
References 
Authors
0
1
Name
Order
Citations
PageRank
David Elliot Shaw1890139.33