Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods

Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods

Abstract: In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we performed var...

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Main Authors: Chang-Guo Zhang, Jaroslav KoÄÂa, Radka Svobodová Vařeková
Format: Article
Language:English
Published: MDPI AG 2004-04-01
Series:International Journal of Molecular Sciences
Subjects:
Van der Waals energy
electrostatic energy
convergence of energy
PME
cutoff method
Online Access:http://www.mdpi.com/1422-0067/5/4/154/
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spelling doaj-f547ba5eb684471499560177faade5322020-11-24T20:59:45ZengMDPI AGInternational Journal of Molecular Sciences1422-00672004-04-015415417310.3390/i5040154Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff MethodsChang-Guo ZhangJaroslav KoÄÂaRadka Svobodová VařekováAbstract: In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we performed various calculations on various representative biological molecules, including seven peptides and proteins, eleven oligonucleotides, and three conformations of a nucleotide-sugar. The results provide useful insights into the appropriate choice of the methods (i.e. the cutoff or PME) and that of the cutoff values for the calculations on different kinds of molecules. It has also been demonstrated that for some cases using different cutoff values for calculating the electrostatic and van der Waals interaction energies will be computationally more efficient.http://www.mdpi.com/1422-0067/5/4/154/Van der Waals energyelectrostatic energyconvergence of energyPMEcutoff method
collection DOAJ
language English
format Article
sources DOAJ
author Chang-Guo Zhang
Jaroslav KoÄÂa
Radka Svobodová Vařeková
spellingShingle Chang-Guo Zhang
Jaroslav KoÄÂa
Radka Svobodová Vařeková
Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods
International Journal of Molecular Sciences
Van der Waals energy
electrostatic energy
convergence of energy
PME
cutoff method
author_facet Chang-Guo Zhang
Jaroslav KoÄÂa
Radka Svobodová Vařeková
author_sort Chang-Guo Zhang
title Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods
title_short Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods
title_full Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods
title_fullStr Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods
title_full_unstemmed Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods
title_sort complexity and convergence of electrostatic and van der waals energies within pme and cutoff methods
publisher MDPI AG
series International Journal of Molecular Sciences
issn 1422-0067
publishDate 2004-04-01
description Abstract: In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we performed various calculations on various representative biological molecules, including seven peptides and proteins, eleven oligonucleotides, and three conformations of a nucleotide-sugar. The results provide useful insights into the appropriate choice of the methods (i.e. the cutoff or PME) and that of the cutoff values for the calculations on different kinds of molecules. It has also been demonstrated that for some cases using different cutoff values for calculating the electrostatic and van der Waals interaction energies will be computationally more efficient.
topic Van der Waals energy
electrostatic energy
convergence of energy
PME
cutoff method
url http://www.mdpi.com/1422-0067/5/4/154/
work_keys_str_mv AT changguozhang complexityandconvergenceofelectrostaticandvanderwaalsenergieswithinpmeandcutoffmethods
AT jaroslavkoaaa complexityandconvergenceofelectrostaticandvanderwaalsenergieswithinpmeandcutoffmethods
AT radkasvobodovaƒavaaaekovaƒa complexityandconvergenceofelectrostaticandvanderwaalsenergieswithinpmeandcutoffmethods
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