Literature DB >> 33858159

Multilevel summation for periodic electrostatics using B-splines.

Hüseyin Kaya1, David J Hardy2, Robert D Skeel3.   

Abstract

Fast methods for calculating two-body interactions have many applications, and for molecular science and cosmology, it is common to employ periodic boundary conditions. However, for the 1/r potential, the energy and forces are ill-defined. Adopted here is the model given by the classic Ewald sum. For the fast calculation of two-body forces, the most celebrated method is the fast multipole method and its tree-code predecessor. However, molecular simulations typically employ mesh-based approximations and the fast Fourier transform. Both types of methods have significant drawbacks, which, in most respects, are overcome by the less well-known multilevel summation method (MSM). Presented here is a realization of the MSM, which can be regarded as a multilevel extension of the (smoothed) particle mesh Ewald (PME) method, but with the Ewald softening replaced by one having a finite range. The two-level (single-grid) version of MSM requires fewer tuning parameters than PME and is marginally faster. Additionally, higher-level versions of MSM scale well to large numbers of processors, whereas PME and other two-level methods do not. Although higher-level versions of MSM are less efficient on a single processor than the two-level version, evidence suggests that they are more efficient than other methods that scale well, such as the fast multipole method and tree codes.

Entities:  

Year:  2021        PMID: 33858159      PMCID: PMC8036131          DOI: 10.1063/5.0040925

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


  13 in total

1.  MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms.

Authors:  Yoshimichi Andoh; Noriyuki Yoshii; Kazushi Fujimoto; Keisuke Mizutani; Hidekazu Kojima; Atsushi Yamada; Susumu Okazaki; Kazutomo Kawaguchi; Hidemi Nagao; Kensuke Iwahashi; Fumiyasu Mizutani; Kazuo Minami; Shin-Ichi Ichikawa; Hidemi Komatsu; Shigeru Ishizuki; Yasuhiro Takeda; Masao Fukushima
Journal:  J Chem Theory Comput       Date:  2013-06-21       Impact factor: 6.006

2.  Correcting Mesh-Based Force Calculations to Conserve Both Energy and Momentum in Molecular Dynamics Simulations.

Authors:  Robert D Skeel; David J Hardy; James C Phillips
Journal:  J Comput Phys       Date:  2007-07-01       Impact factor: 3.553

3.  Extension and evaluation of the multilevel summation method for fast long-range electrostatics calculations.

Authors:  Stan G Moore; Paul S Crozier
Journal:  J Chem Phys       Date:  2014-06-21       Impact factor: 3.488

4.  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

5.  An Exact Ewald Summation Method in Theory and Practice.

Authors:  S Stenberg; B Stenqvist
Journal:  J Phys Chem A       Date:  2020-05-05       Impact factor: 2.781

6.  Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Authors:  James C Phillips; David J Hardy; Julio D C Maia; John E Stone; João V Ribeiro; Rafael C Bernardi; Ronak Buch; Giacomo Fiorin; Jérôme Hénin; Wei Jiang; Ryan McGreevy; Marcelo C R Melo; Brian K Radak; Robert D Skeel; Abhishek Singharoy; Yi Wang; Benoît Roux; Aleksei Aksimentiev; Zaida Luthey-Schulten; Laxmikant V Kalé; Klaus Schulten; Christophe Chipot; Emad Tajkhorshid
Journal:  J Chem Phys       Date:  2020-07-28       Impact factor: 3.488

7.  The u-series: A separable decomposition for electrostatics computation with improved accuracy.

Authors:  Cristian Predescu; Adam K Lerer; Ross A Lippert; Brian Towles; J P Grossman; Robert M Dirks; David E Shaw
Journal:  J Chem Phys       Date:  2020-02-28       Impact factor: 3.488

8.  Periodic Coulomb Tree Method: An Alternative to Parallel Particle Mesh Ewald.

Authors:  Henry A Boateng
Journal:  J Chem Theory Comput       Date:  2019-12-09       Impact factor: 6.006

9.  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

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