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  • 1
    ISSN: 0192-8651
    Keywords: molecular dynamics ; protein dynamics ; fast electrostatics computation ; fast multipole method ; multiple-time-step method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Within molecular dynamics simulations of protein-solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. Conventional truncation methods circumvent that computational problem, but are hampered by serious artifacts concerning structure and dynamics of the simulated systems. To avoid these artifacts we have developed an efficient and yet sufficiently accurate approximation scheme which combines the structure-adapted multipole method (SAMM) [C. Niedermeier and P. Tavan, J. Chem. Phys., 101, 734 (1994)] with a multiple-time-step method. The computational effort for MD simulations required within our fast multiple-time-step structure-adapted multipole method (FAMUSAMM) scales linearly with the number of particles. For a system with 36,000 atoms we achieve a computational speed-up by a factor of 60 as compared with the exact evaluation of the Coulomb forces. Extended test simulations show that the applied approximations do not seriously affect structural or dynamical properties of the simulated systems.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1729-1749, 1997
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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