Molecular mechanics and dynamics of biomolecules using a solvent continuum model

F. Fogolari, G. Esposito, P. Viglino, H. Molinari

Research output: Contribution to journalArticlepeer-review

Abstract

An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations.

Original languageEnglish (US)
Pages (from-to)1830-1842
Number of pages13
JournalJournal of Computational Chemistry
Volume22
Issue number15
DOIs
StatePublished - Nov 30 2001

Keywords

  • Continuum electrostatics
  • Implicit solvent
  • Molecular dynamics
  • Poisson-Boltzmann
  • Solvent-accessible surface area

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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