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

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.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-54BC-6 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-C4B3-1
Genre: Journal Article

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 Creators:
Eichinger, M., Author
Grubmüller, H.1, Author              
Heller, H., Author
Tavan, P., Author
Affiliations:
1Research Group of Theoretical Molecular Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578630              

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Free keywords: molecular dynamics; protein dynamics; fast electrostatics computation; fast multipole method; multiple-time-step method
 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.

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Language(s): eng - English
 Dates: 1998-12-071997-11-15
 Publication Status: Published in print
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Title: Journal of Computational Chemistry
Source Genre: Journal
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Publ. Info: New York : Wiley.
Pages: - Volume / Issue: 18 (14) Sequence Number: - Start / End Page: 1729 - 1749 Identifier: ISSN: 0192-8651
CoNE: https://pure.mpg.de/cone/journals/resource/954925489848