| 472 A HIGH PERFORMANCE SYSTEM FOR MOLECULAR DYNAMICS SIMULATION OF BIOMOLECULES USING A SPECIAL-PURPOSE COMPUTER (2009) | |||||||||||||
Abstract | |||||||||||||
| GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performanceof MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to-6 Gflops. The precision of MD-GRAPE was goodjudging from the acceptable fluctuation of the total energy. Then a software named PEACH (Program for Energetic Analysis of bioCHemical molecules) was developed for molecular dynamics of biomolecules in combination with MD-GRAPE. Molecular dynamics simulation was performed for several protein-solvent systems with different sizes. Simulation of the largest system investigated (27,000 atoms) took only 5 see/step. Thus, the PEACH-GRAPE system is expected to be useful in accurate and reliable simulationof largebiomolecules. 1 | |||||||||||||
Details der Publikation | |||||||||||||
| |||||||||||||