Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations
✍ Scribed by Toyoda, Shinjiro; Miyagawa, Hiroh; Kitamura, Kunihiro; Amisaki, Takashi; Hashimoto, Eiri; Ikeda, Hitoshi; Kusumi, Akihiro; Miyakawa, Nobuaki
- Publisher
- John Wiley and Sons
- Year
- 1999
- Tongue
- English
- Weight
- 336 KB
- Volume
- 20
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
computer. The force is calculated with sufficient accuracy for practical MD simulations. The processor also calculates virials simultaneously with forces for use in the calculation of pressure, accommodates periodic boundary conditions, and can be used in Ewald summations. An MD Engine system consisting of 76 processors calculates nonbonded interactions about 50 times faster than an Ž . Ž UltraSPARC-I processor Sun Ultra-2, 200 MHz or an R10000 processor SGI . Origin 200, 180 MHz . On a Sun Ultra-2 workstation with a single UltraSPARC-I processor an MD simulation of a Ras p21 protein molecule immersed in a water Ž .