FAST AND ACCURATE MOLECULAR-DYNAMICS SIMULATION OF A PROTEIN USING A SPECIAL-PURPOSE COMPUTER

The rapid and accurate molecular dynamics simulation of biomolecules w as made possible by a special purpose computer, MD-GRAPE (GRAvity PipE for Molecular Dynamics), which computes arbitrary central force and p otential. A program package for the molecular dynamics simulation of b iological macromolecules was developed (PEACH Program for Energetic An alysis of bioCHemical molecules), which used MD-GRAPE for computation of the nonbonded interactions (van der Waals, and direct or Ewald summ ation of the electrostatic) without a cutoff scheme. A multiple time s tep integrator from the literture was implemented in PEACH to save com putation time. Nanosecond order molecular dynamics simulations of a fu lly solvated histidine-containing phosphocarrier protein (similar to 1 0,000 atoms) were performed in a spherical (direct summation of the el ectrostatic) or a periodic (Ewald summation) boundary with or without Nose-Hoover isothermal algorithm. The trajectories thus obtained witho ut the nonbonded cutoff were quite stable, indicating the usefulness o f the PEACH-GRAPE system constructed in this study. (C) 1997 John Wile y & Sons, Inc.