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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...
CASES
2007
ACM
14 years 16 days ago
An integrated ARM and multi-core DSP simulator
In this paper we describe the design and implementation of a flexible, and extensible, just-in-time ARM simulator designed to run co-operatively with a multi-core DSP simulator on...
Sharad Singhai, MingYung Ko, Sanjay Jinturkar, May...
PPOPP
2006
ACM
14 years 2 months ago
Performance characterization of molecular dynamics techniques for biomolecular simulations
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations...
Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwa...
SC
1995
ACM
14 years 2 days ago
I/O Limitations in Parallel Molecular Dynamics
Abstract We discuss data production rates and their impact on the performance of scientific applications using parallel computers. On one hand, too high rates of data production c...
Terry W. Clark, L. Ridgway Scott, Stanislaw Wloked...
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...