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Validation of the 53A6 GROMOS force field

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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.

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Acknowledgments

Professor Dr. K. Wüthrich is gratefully acknowledged for making the experimental data on the β3-dodecamer available. We also thank Lorna Smith for helpful discussions on the NOE analysis. Financial support by the National Center of Competence in Research (NCCR) in Structural Biology of the Swiss National Science Foundation (SNSF) is gratefully acknowledged.

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Authors and Affiliations

  1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093, Zurich, Switzerland

    Chris Oostenbrink, Thereza A. Soares & Wilfred F. van Gunsteren

  2. Computational Chemistry, Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany

    Nico F. A. van der Vegt

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  1. Chris Oostenbrink
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  2. Thereza A. Soares
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  3. Nico F. A. van der Vegt
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  4. Wilfred F. van Gunsteren
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Correspondence to Wilfred F. van Gunsteren.

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Oostenbrink, C., Soares, T.A., van der Vegt, N.F.A. et al. Validation of the 53A6 GROMOS force field. Eur Biophys J 34, 273–284 (2005). https://doi.org/10.1007/s00249-004-0448-6

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