Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer

The rapid and accurate molecular dynamics simulation of biomolecules was made possible by a special purpose computer, MD-GRAPE (GRAvity PipE for Molecular Dynamics), which computes arbitrary central force and potential. A program package for the molecular dynamics simulation of biological macromolecules was developed (PEACH Program for Energetic Analysis of bioCHemical molecules), which used MD-GRAPE for computation of the nonbonded interactions (van der Waals, and direct or Ewald summation of the electrostatic) without a cutoff scheme. A multiple time step integrator from the literture was implemented in PEACH to save computation time. Nanosecond order molecular dynamics simulations of a fully solvated histidine-containing phosphocarrier protein (∼10,000 atoms) were performed in a spherical (direct summation of the electrostatic) or a periodic (Ewald summation) boundary with or without Nose–Hoover isothermal algorithm. The trajectories thus obtained without the nonbonded cutoff were quite stable, indicating the usefulness of the PEACH-GRAPE system constructed in this study.