Abstract
Many realistic biomolecular simulations require use of periodic boundary conditions to create a surface-free environment for the molecule of interest and associated solvent molecules to interact. Electrostatic interactions are the principal computational cost of such simulations. We have implemented two codes: a parallel variant of an Ewald summation method which computes the effect of infinite periodic boundary conditions, and a parallel variant of a multipole algorithm which explicitly computes the interactions within a large but finite periodic system. Each has a regime of applicability, with Ewald favoring smaller systems and fewer processors, and the multipole methods favoring larger systems and more processors. Simulations can now include a full treatment of periodic electrostatics to three or four significant figures of accuracy for a computational cost equivalent to that of a 12Å cutoff simulation.
Supported by NSF ASC-9318159, NSF CDA-9422065, NIH Research Resource RR08102, and computer time from the North Carolina Supercomputing Center. An earlier version of this paper was presented at the Eighth SIAM Conference on Parallel Processing for Scientific Computing.
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© 1999 Springer-Verlag Berlin Heidelberg
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Board, J.A., Humphres, C.W., Lambert, C.G., Rankin, W.T., Toukmaji, A.Y. (1999). Ewald and Multipole Methods for Periodic N-Body Problems. In: Deuflhard, P., Hermans, J., Leimkuhler, B., Mark, A.E., Reich, S., Skeel, R.D. (eds) Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-58360-5_27
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DOI: https://doi.org/10.1007/978-3-642-58360-5_27
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