Literature DB >> 33088167

FAST UPDATING MULTIPOLE COULOMBIC POTENTIAL CALCULATION.

Thomas A HÖft1, Bradley K Alpert2.   

Abstract

We present a numerical method to efficiently and accurately re-compute the Coulomb potential of a large ensemble of charged particles after a subset of the particles undergoes a change of position. Errors are bounded even after a large number of such shifts, making it practical for use in Monte Carlo Markov chain methods in molecular dynamics, computational astrophysics, computational chemistry, and other applications. The method uses truncated multipole expansions of the potential energy functional and a tree decomposition of the computational domain to reduce the computational complexity. Computational costs scale logarithmically in the size of the problem. Scaling, accuracy, and efficiency are confirmed with numerical experiments. The new method outperforms a direct calculation for moderate problem sizes.

Entities:  

Keywords:  35J05; 35Q60; 65E05; 68W25; 70F10; 78M16; 92C40; 92E10; Laplace equation; N-body problem; fast multipole method; molecular dynamics; potential theory

Year:  2017        PMID: 33088167      PMCID: PMC7574401     

Source DB:  PubMed          Journal:  SIAM J Sci Comput        ISSN: 1064-8275            Impact factor:   2.373


  13 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

2.  Protein structure prediction and structural genomics.

Authors:  D Baker; A Sali
Journal:  Science       Date:  2001-10-05       Impact factor: 47.728

Review 3.  Molecular dynamics simulations of biomolecules.

Authors:  Martin Karplus; J Andrew McCammon
Journal:  Nat Struct Biol       Date:  2002-09

4.  Randomized algorithms for the low-rank approximation of matrices.

Authors:  Edo Liberty; Franco Woolfe; Per-Gunnar Martinsson; Vladimir Rokhlin; Mark Tygert
Journal:  Proc Natl Acad Sci U S A       Date:  2007-12-04       Impact factor: 11.205

5.  Fast multipole methods for particle dynamics.

Authors:  J Kurzak; B M Pettitt
Journal:  Mol Simul       Date:  2006       Impact factor: 2.178

Review 6.  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

Review 7.  Biomolecularmodeling and simulation: a field coming of age.

Authors:  Tamar Schlick; Rosana Collepardo-Guevara; Leif Arthur Halvorsen; Segun Jung; Xia Xiao
Journal:  Q Rev Biophys       Date:  2011-05       Impact factor: 5.318

8.  ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 8. Properties of material streams and solvent design.

Authors:  Vladimir Diky; Robert D Chirico; Chris D Muzny; Andrei F Kazakov; Kenneth Kroenlein; Joseph W Magee; Ilmutdin Abdulagatov; Jeong Won Kang; Rafiqul Gani; Michael Frenkel
Journal:  J Chem Inf Model       Date:  2012-12-19       Impact factor: 4.956

9.  Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations.

Authors:  Magnus Schwörer; Konstantin Lorenzen; Gerald Mathias; Paul Tavan
Journal:  J Chem Phys       Date:  2015-03-14       Impact factor: 3.488

10.  Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions.

Authors:  M Patra; M Karttunen; M T Hyvönen; E Falck; P Lindqvist; I Vattulainen
Journal:  Biophys J       Date:  2003-06       Impact factor: 4.033

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