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IRREGULAR
1998
Springer
13 years 9 months ago
Modeling Dynamic Load Balancing in Molecular Dynamics to Achieve Scalable Parallel Execution
To achieve scalable parallel performance in Molecular Dynamics Simulation, we have modeled and implemented several dynamic spatial domain decomposition algorithms. The modeling is ...
Lars S. Nyland, Jan Prins, Ru Huai Yun, Jan Herman...
CPHYSICS
2008
106views more  CPHYSICS 2008»
13 years 5 months ago
A space-time-ensemble parallel nudged elastic band algorithm for molecular kinetics simulation
A scalable parallel algorithm has been designed to study long-time dynamics of many-atom systems based on the nudged elastic band method, which performs mutually constrained molec...
Aiichiro Nakano
ASAP
2009
IEEE
142views Hardware» more  ASAP 2009»
14 years 2 months ago
Parallel Discrete Event Simulation of Molecular Dynamics Through Event-Based Decomposition
—Molecular dynamics simulation based on discrete event simulation (DMD) is emerging as an alternative to time-step driven molecular dynamics (MD). DMD uses simplified discretize...
Martin C. Herbordt, Md. Ashfaquzzaman Khan, Tony D...
ICS
2009
Tsinghua U.
13 years 11 months ago
Dynamic topology aware load balancing algorithms for molecular dynamics applications
Molecular Dynamics applications enhance our understanding of biological phenomena through bio-molecular simulations. Large-scale parallelization of MD simulations is challenging b...
Abhinav Bhatele, Laxmikant V. Kalé, Sameer ...
PPOPP
2006
ACM
13 years 11 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...