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A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field

European Biophysics Journal volume 32, pages 67–77 (2003)Cite this article

Abstract

The performance of the GROMOS96 parameter set 45A3 developed for aliphatic alkanes is tested on a bilayer of dipalmitoylphosphatidylcholine (DPPC) in water in the liquid-crystalline Lα phase. Variants of the force-field parameter set as well as different sets of simulation conditions or simulation parameter sets are evaluated. In the case of the force-field parameters, the van der Waals constants for the non-bonded interaction of the ester carbonyl carbon and the partial charges and charge group definition of the phosphatidylcholine head group are examined. On the methodological side, different cut-off distances for the non-bonded interactions, use of a reaction-field force due to long-range electrostatic interactions, the frequency of removal of the centre of mass motion and the strength of the coupling of the pressure of the system to the pressure bath are tested. The area per lipid, as a measure of structure, the order parameters of the chain carbons, as a measure of membrane fluidity, and the translational diffusion of the lipids in the plane of the bilayer are calculated and compared with experimental values. An optimal set of simulation parameters for which the GROMOS96 parameter set 45A3 yields a head group area, chain order parameters and a lateral diffusion coefficient in accordance with the experimental data is listed.

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Acknowledgements

D.P.T. is a Scholar of the Alberta Heritage Foundation for Medical Research. Financial support by the National Center of Competence in Research (NCCR) Structural Biology of the Swiss National Science Foundation is gratefully acknowledged.

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Authors and Affiliations

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

    Indira Chandrasekhar, Mika Kastenholz, Roberto D. Lins, Chris Oostenbrink, Lukas D. Schuler & Wilfred F. van Gunsteren

  2. Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta , T2N 1N4, Canada

    D. Peter Tieleman

Authors
  1. Indira Chandrasekhar
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  2. Mika Kastenholz
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  3. Roberto D. Lins
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  4. Chris Oostenbrink
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  6. D. Peter Tieleman
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  7. Wilfred F. van Gunsteren
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Correspondence to Indira Chandrasekhar.

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Chandrasekhar, I., Kastenholz, M., Lins, R.D. et al. A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field. Eur Biophys J 32, 67–77 (2003). https://doi.org/10.1007/s00249-002-0269-4

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  • DOI: https://doi.org/10.1007/s00249-002-0269-4

Keywords

  • Molecular dynamics simulation
  • Lipids
  • Potential energy parameters
  • GROMOS