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IPPS
2006
IEEE
13 years 9 months ago
Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L
The Replica Exchange method is a popular approach for studying the folding thermodynamics of small to modest size proteins in explicit solvent, since it is easily parallelized. Ho...
Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. P...
ICPP
2006
IEEE
13 years 9 months ago
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications
— This paper presents Salsa, a novel, decentralized and asynchronous realization of the “replica exchange” algorithm for simulating the structure, function, folding, and dyna...
Li Zhang, Manish Parashar, Emilio Gallicchio, Rona...
PPOPP
2006
ACM
13 years 9 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...
IJHPCA
2008
131views more  IJHPCA 2008»
13 years 3 months ago
De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers
We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and ...
Aiichiro Nakano, Rajiv K. Kalia, Ken-ichi Nomura, ...
ICS
2004
Tsinghua U.
13 years 9 months ago
Adaptive incremental checkpointing for massively parallel systems
Given the scale of massively parallel systems, occurrence of faults is no longer an exception but a regular event. Periodic checkpointing is becoming increasingly important in the...
Saurabh Agarwal, Rahul Garg, Meeta Sharma Gupta, J...