Molecular dynamics is a powerful technique used to obtain static or dynamic properties of liquids and solids. The sheer computational intensity of many of these simulations demands more computational power than what any uniprocessor system can provide. Fortunately, these simulations can be parallelized, allowing faster execution times on a cluster of workstations. Of late, custom VLSI chips have been designed to provide an alternative to parallel techniques. The MD-GRAPE 2 is one such solution, offering a peak performance of 64 Gflops. We evaluate the performance and cost-effectiveness of various methods used in sequential and parallel molecular dynamics and the MD-GRAPE 2. We then illustrate how MD simulations involving more complex potential functions can be scheduled on parallel machines and the MD-GRAPE 2 simultaneously.
|Original language||English (US)|
|Number of pages||10|
|Journal||Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|
|Publication status||Published - Dec 1 2004|
ASJC Scopus subject areas
- Theoretical Computer Science
- Computer Science(all)