European Biophysics Journal

, Volume 34, Issue 4, pp 273–284 | Cite as

Validation of the 53A6 GROMOS force field

  • Chris Oostenbrink
  • Thereza A. Soares
  • Nico F. A. van der Vegt
  • Wilfred F. van Gunsteren
Article

Abstract

The quality of biomolecular dynamics simulations relies critically on the force field that is used to describe the interactions between particles in the system. Force fields, which are generally parameterized using experimental data on small molecules, can only prove themselves in realistic simulations of relevant biomolecular systems. In this work, we begin the validation of the new 53A6 GROMOS parameter set by examining three test cases. Simulations of the well-studied 129 residue protein hen egg-white lysozyme, of the DNA dodecamer d(CGCGAATTCGCG)2, and a proteinogenic β3-dodecapeptide were performed and analysed. It was found that the new parameter set performs as well as the previous parameter sets in terms of protein (45A3) and DNA (45A4) stability and that it is better at describing the folding–unfolding balance of the peptide. The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterized.

Keywords

GROMOS Force field Molecular dynamics simulation DNA Lysozyme β-Peptide 

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Copyright information

© EBSA 2005

Authors and Affiliations

  • Chris Oostenbrink
    • 1
  • Thereza A. Soares
    • 1
  • Nico F. A. van der Vegt
    • 2
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Laboratory of Physical ChemistrySwiss Federal Institute of TechnologyZurichSwitzerland
  2. 2.Computational ChemistryMax-Planck-Institute for Polymer ResearchMainzGermany

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