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» I O Limitations in Parallel Molecular Dynamics
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ICPP
2006
IEEE
13 years 11 months ago
Scalable Time-Parallelization of Molecular Dynamics Simulations in Nano Mechanics
— Molecular Dynamics (MD) is an important atomistic simulation technique, with widespread use in computational chemistry, biology, and materials. An important limitation of MD is...
Yanan Yu, Ashok Srinivasan, Namas Chandra
ICCD
2008
IEEE
119views Hardware» more  ICCD 2008»
14 years 2 months ago
Hierarchical simulation-based verification of Anton, a special-purpose parallel machine
—One of the major design verification challenges in the development of Anton, a massively parallel special-purpose machine for molecular dynamics, was to provide evidence that co...
John P. Grossman, John K. Salmon, Richard C. Ho, D...
ISCA
2007
IEEE
196views Hardware» more  ISCA 2007»
13 years 12 months ago
Anton, a special-purpose machine for molecular dynamics simulation
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 ...
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Je...
SPAA
2009
ACM
14 years 6 months ago
Dynamic external hashing: the limit of buffering
Hash tables are one of the most fundamental data structures in computer science, in both theory and practice. They are especially useful in external memory, where their query perf...
Zhewei Wei, Ke Yi, Qin Zhang
ANSS
2007
IEEE
13 years 9 months ago
MDL, A Domain-Specific Language for Molecular Dynamics
Molecular Dynamics (MD) involves solving Newton's equations of motion for a molecular system and propagating the system by time-dependent updates of atomic positions and velo...
Trevor M. Cickovski, Chris Sweet, Jesús A. ...