Complexity and convergence of electrostatic and van der Waals energies within PME and cutoff methods

Radka Svobodov́ Vařekov́, Jaroslav Koča, Chang Guo Zhan

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

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.

Original languageEnglish
Pages (from-to)154-173
Number of pages20
JournalInternational Journal of Molecular Sciences
Volume5
Issue numberSPEC ISS
DOIs
StatePublished - Apr 2004

Keywords

  • Convergence of energy
  • Cutoff method
  • Electrostatic energy
  • PME
  • Van der Waals energy

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

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