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Theoretical Chemistry Accounts

, Volume 101, Issue 1–3, pp 163–169 | Cite as

Poisson-Boltzmann calculations versus molecular dynamics simulations for calculating the electrostatic potential of a solvated peptide

  • Gerald Löffler
Regular article

Abstract.

We performed a very long molecular dynamics simulation of a peptide in explicit water molecules and ions and averaged the electrostatic potential caused by peptide, water and ions at eight points in the vicinity of the peptide. These electrostatic potential values were directly compared to the potential calculated by solving the non-linear Poisson-Boltzmann equation for the system, which describes the solvent using continuum electrostatics. We analyze the contribution of dielectric constant, conformational flexibility and solvation effects on the electrostatic potential at these eight points.

Key words: Protein Solvation model Electrostatic potential Molecular dynamics simulation Continuum electrostatics Poisson-Boltzmann equation 

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Copyright information

© Springer-Verlag Berlin Heidelberg 1999

Authors and Affiliations

  • Gerald Löffler
    • 1
  1. 1.Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria (Gerald.Loeffler@vienna.at)AT

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