Journal of Molecular Modeling

, 23:259 | Cite as

Modeling DMPC lipid membranes with SIRAH force-field

  • Exequiel E. Barrera
  • Ezequiel N. Frigini
  • Rodolfo D. Porasso
  • Sergio Pantano
Original Paper
Part of the following topical collections:
  1. QUITEL 2016

Abstract

Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations (http://www.sirahff.com). We show that the present model not only achieves a correct reproduction of structural parameters as area per lipid and thickness, but also dynamic descriptors such as diffusion coefficient, order parameters, and proper temperature driven variations. Adding phospholipid membranes to the existing aqueous solution, protein and DNA representations of the SIRAH force field permit considering the most common problems tackled by the biomolecular simulation community.

Keywords

Coarse-grained models DMPC Lipid membranes Molecular dynamics 

Notes

Acknowledgments

This work was partially funded by FOCEM (MERCOSUR Structural Convergence Fund), COF 03/11. S.P. is researcher of the National Scientific Program of ANII (SNI). E.E.B. is beneficiary of a postdoctoral fellowship of CONICET. E.N.F. is beneficiary of a doctoral fellowship of CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Exequiel E. Barrera
    • 1
  • Ezequiel N. Frigini
    • 2
  • Rodolfo D. Porasso
    • 2
  • Sergio Pantano
    • 1
  1. 1.Biomolecular Simulations Group, Institut Pasteur de MontevideoMontevideoUruguay
  2. 2.Instituto de Matemática Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y NaturalesUniversidad Nacional de San LuisSan LuisArgentina

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