ISSN:
0192-8651
Schlagwort(e):
molecular dynamics
;
special-purpose computer
;
multiple time step method
;
electrostatic interaction
;
HPr
;
Chemistry
;
Theoretical, Physical and Computational Chemistry
Quelle:
Wiley InterScience Backfile Collection 1832-2000
Thema:
Chemie und Pharmazie
,
Informatik
Notizen:
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
Zusätzliches Material:
8 Ill.
Materialart:
Digitale Medien
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