Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it i
Scalable molecular dynamics with NAMD
✍ Scribed by James C. Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D. Skeel; Laxmikant Kalé; Klaus Schulten
- Publisher
- John Wiley and Sons
- Year
- 2005
- Tongue
- English
- Weight
- 977 KB
- Volume
- 26
- Category
- Article
- ISSN
- 0192-8651
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To achieve scalable parallel performance in molecular dynamics simulations, we have modeled and implemented several dynamic spatial domain decomposition algorithms. The modeling is based upon the bulk synchronous parallel architecture model (BSP), which describes supersteps of computation, communica
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