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Journal Article

FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations.

MPS-Authors
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Grubmüller,  H.
Research Group of Theoretical Molecular Biophysics, MPI for biophysical chemistry, Max Planck Society;

Fulltext (public)

1836557.pdf
(Publisher version), 433KB

Supplementary Material (public)

Eichinger_famusamm.html
(Supplementary material), 6KB

Eichinger_famusamm.ps
(Supplementary material), 9MB

Citation

Eichinger, M., Grubmüller, H., Heller, H., & Tavan, P. (1997). FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations. Journal of Computational Chemistry, 18(14), 1729-1749.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0014-54BC-6
Abstract
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.