Journal of Biomolecular NMR

, 51:265 | Cite as

Biomolecular structure refinement using the GROMOS simulation software

  • Nathan Schmid
  • Jane R. Allison
  • Jožica Dolenc
  • Andreas P. Eichenberger
  • Anna-Pitschna E. Kunz
  • Wilfred F. van Gunsteren


For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, 3 J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.


GROMOS Structure refinement Crystallography NMR 



We thank Robert Best for providing his RDC singular value decomposition code and Kevin Cowtan for advice on how to compute gradients using the Clipper libraries. In addition, contributions from Markus Christen, Fabian Freitag, Bruno Horta, Bettina Keller, Chris Oostenbrink, Christine Peter, Maxime Richard and Alex de Vries are gratefully acknowledged. This work was financially supported by the National Center of Competence in Research (NCCR) in Structural Biology and by grant number 200020-121913 of the Swiss National Science Foundation, and by grant number 228076 of the European Research Council, which is gratefully acknowledged.


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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Nathan Schmid
    • 1
  • Jane R. Allison
    • 1
  • Jožica Dolenc
    • 1
    • 2
  • Andreas P. Eichenberger
    • 1
  • Anna-Pitschna E. Kunz
    • 1
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Laboratory of Physical ChemistrySwiss Federal Institute of Technology ETHZürichSwitzerland
  2. 2.Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia

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