Literature DB >> 24437863

Multilevel summation for dispersion: a linear-time algorithm for r(-6) potentials.

Daniel Tameling1, Paul Springer1, Paolo Bientinesi1, Ahmed E Ismail1.   

Abstract

We have extended the multilevel summation (MLS) method, originally developed to evaluate long-range Coulombic interactions in molecular dynamics simulations [R. D. Skeel, I. Tezcan, and D. J. Hardy, J. Comput. Chem. 23, 673 (2002)], to handle dispersion interactions. While dispersion potentials are formally short-ranged, accurate calculation of forces and energies in interfacial and inhomogeneous systems require long-range methods. The MLS method offers some significant advantages compared to the particle-particle particle-mesh and smooth particle mesh Ewald methods. Unlike mesh-based Ewald methods, MLS does not use fast Fourier transforms and is thus not limited by communication and bandwidth concerns. In addition, it scales linearly in the number of particles, as compared with the O(NlogN) complexity of the mesh-based Ewald methods. While the structure of the MLS method is invariant for different potentials, every algorithmic step had to be adapted to accommodate the r(-6) form of the dispersion interactions. In addition, we have derived error bounds, similar to those obtained by Hardy ["Multilevel summation for the fast evaluation of forces for the simulation of biomolecules," Ph.D. thesis, University of Illinois at Urbana-Champaign, 2006] for the electrostatic MLS. Using a prototype implementation, we have demonstrated the linear scaling of the MLS method for dispersion, and present results establishing the accuracy and efficiency of the method.

Entities:  

Year:  2014        PMID: 24437863     DOI: 10.1063/1.4857735

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  4 in total

1.  Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations.

Authors:  David J Hardy; Matthew A Wolff; Jianlin Xia; Klaus Schulten; Robert D Skeel
Journal:  J Chem Phys       Date:  2016-03-21       Impact factor: 3.488

2.  Multilevel summation for periodic electrostatics using B-splines.

Authors:  Hüseyin Kaya; David J Hardy; Robert D Skeel
Journal:  J Chem Phys       Date:  2021-04-14       Impact factor: 3.488

3.  Multilevel summation method for electrostatic force evaluation.

Authors:  David J Hardy; Zhe Wu; James C Phillips; John E Stone; Robert D Skeel; Klaus Schulten
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

Review 4.  Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors.

Authors:  Anu George; Sandip Mondal; Madhura Purnaprajna; Prashanth Athri
Journal:  ACS Omega       Date:  2022-09-08
  4 in total

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