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. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1546–1563, 1997

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