Literature DB >> 19194526

Fast multipole methods for particle dynamics.

J Kurzak1, B M Pettitt.   

Abstract

The growth of simulations of particle systems has been aided by advances in computer speed and algorithms. The adoption of O(N) algorithms to solve N-body simulation problems has been less rapid due to the fact that such scaling was only competitive for relatively large N. Our work seeks to find algorithmic modifications and practical implementations for intermediate values of N in typical use for molecular simulations. This article reviews fast multipole techniques for calculation of electrostatic interactions in molecular systems. The basic mathematics behind fast summations applied to long ranged forces is presented along with advanced techniques for accelerating the solution, including our most recent developments. The computational efficiency of the new methods facilitates both simulations of large systems as well as longer and therefore more realistic simulations of smaller systems.

Year:  2006        PMID: 19194526      PMCID: PMC2634295          DOI: 10.1080/08927020600991161

Source DB:  PubMed          Journal:  Mol Simul        ISSN: 0892-7022            Impact factor:   2.178


  1 in total

Review 1.  Molecular dynamics simulations of biomolecules: long-range electrostatic effects.

Authors:  C Sagui; T A Darden
Journal:  Annu Rev Biophys Biomol Struct       Date:  1999
  1 in total
  6 in total

Review 1.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

2.  Message-passing implementation of the data diffusion communication model in fast multipole methods: large scale biomolecular simulations.

Authors:  Jakub Kurzak; B Montgomery Pettitt
Journal:  J Algorithm Comput Technol       Date:  2008

3.  AUTOMATIC GENERATION OF FFT FOR TRANSLATIONS OF MULTIPOLE EXPANSIONS IN SPHERICAL HARMONICS.

Authors:  Jakub Kurzak; Dragan Mirkovic; B Montgomery Pettitt; S Lennart Johnsson
Journal:  Int J High Perform Comput Appl       Date:  2008-01-01       Impact factor: 1.942

4.  The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2019-06-07       Impact factor: 3.488

5.  Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor.

Authors:  Xiongwu Wu; Frank C Pickard; Bernard R Brooks
Journal:  J Chem Phys       Date:  2016-10-28       Impact factor: 3.488

6.  FAST UPDATING MULTIPOLE COULOMBIC POTENTIAL CALCULATION.

Authors:  Thomas A HÖft; Bradley K Alpert
Journal:  SIAM J Sci Comput       Date:  2017-06-06       Impact factor: 2.373

  6 in total

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