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FPL
2006
Springer
123views Hardware» more  FPL 2006»
13 years 11 months ago
Improved Interpolation and System Integration for FPGA-Based Molecular Dynamics Simulations
: FPGA-based acceleration of molecular dynamics (MD) has been the subject of several recent studies. Here we describe a new non-bonded force computation pipeline implemented on a 2...
Yongfeng Gu, Tom Van Court, Martin C. Herbordt
CONCURRENCY
1998
115views more  CONCURRENCY 1998»
13 years 7 months ago
Falcon: On-line monitoring for steering parallel programs
Abstract Advances in high performance computing, communications, and user interfaces enable developers to construct increasingly interactive high performance applications. The Falc...
Weiming Gu, Greg Eisenhauer, Karsten Schwan, Jeffr...
FPL
2007
Springer
150views Hardware» more  FPL 2007»
13 years 11 months ago
Discrete Event Simulation of Molecular Dynamics with Configurable Logic
: Molecular dynamics simulation based on discrete event simulation (DMD) is emerging as an alternative to time-step driven molecular dynamics (MD). DMD uses simplified discretized ...
Josh Model, Martin C. Herbordt
JCC
2002
94views more  JCC 2002»
13 years 7 months ago
Modern protein force fields behave comparably in molecular dynamics simulations
: Several molecular dynamics simulations were performed on three proteins--bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and domain IIA of bacillus subtilis glucose pe...
Daniel J. Price, Charles L. Brooks III
ICCD
2008
IEEE
119views Hardware» more  ICCD 2008»
14 years 4 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...