title: A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.
abstract: GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging 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 sec/step. Thus, the PEACH-GRAPE system is expected to be useful in accurate and reliable simulation of large biomolecules.
authors.affiliation: Electrotechnical Laboratory, Ibaraki, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Komeiji
authors.forename: H
authors.initials: H
authors.lastname: Yokoyama
authors.forename: M
authors.initials: M
authors.lastname: Uebayasi
authors.forename: M
authors.initials: M
authors.lastname: Taiji
authors.forename: T
authors.initials: T
authors.lastname: Fukushige
authors.forename: D
authors.initials: D
authors.lastname: Sugimoto
authors.forename: R
authors.initials: R
authors.lastname: Takata
authors.forename: A
authors.initials: A
authors.lastname: Shimizu
authors.forename: K
authors.initials: K
authors.lastname: Itsukashi
mesh_terms: D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D003198:Computer Simulation; D004867:Equipment Design; D008956:Models, Chemical; D008968:Molecular Conformation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software; D012997:Solvents
chemical_list: D011506:Proteins; D012997:Solvents