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CGF
2010
143views more  CGF 2010»
13 years 8 months ago
Coherent Culling and Shading for Large Molecular Dynamics Visualization
Molecular dynamics simulations are a principal tool for studying molecular systems. Such simulations are used to investigate molecular structure, dynamics, and thermodynamical pro...
Sebastian Grottel, Guido Reina, Carsten Dachsbache...
ICCS
2007
Springer
14 years 2 months ago
A General Long-Time Molecular Dynamics Scheme in Atomistic Systems: Hyperdynamics in Entropy Dominated Systems
Abstract. We extend the hyperdynamics method developed for lowdimensional energy-dominated systems, to simulate slow dynamics in more general atomistic systems. We show that a few ...
Xin Zhou, Yi Jiang
IPPS
2008
IEEE
14 years 2 months ago
Model-guided performance tuning of parameter values: A case study with molecular dynamics visualization
In this paper, we consider the interaction between application programmers and tools that automatically search a space of application-level parameters that are believed to impact ...
Yiinju L. Nelson, Bhupesh Bansal, Mary W. Hall, Ai...
JCC
2006
103views more  JCC 2006»
13 years 8 months ago
Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
: The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to...
Oliver F. Lange, Lars V. Schäfer, Helmut Grub...
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...