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Coarse-Grained Force Fields for Molecular Simulations

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Molecular Modeling of Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1215))

Abstract

Molecular dynamics (MD) simulations at the atomic scale are a powerful tool to study the structure and dynamics of model biological systems. However, because of their high computational cost, the time and length scales of atomistic simulations are limited. Biologically important processes, such as protein folding, ion channel gating, signal transduction, and membrane remodeling, are difficult to investigate using atomistic simulations. Coarse-graining reduces the computational cost of calculations by reducing the number of degrees of freedom in the model, allowing simulations of larger systems for longer times. In the first part of this chapter we review briefly some of the coarse-grained models available for proteins, focusing on the specific scope of each model. Then we describe in more detail the MARTINI coarse-grained force field, and we illustrate how to set up and run a simulation of a membrane protein using the Gromacs software package. We explain step-by-step the preparation of the protein and the membrane, the insertion of the protein in the membrane, the equilibration of the system, the simulation itself, and the analysis of the trajectory.

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Acknowledgments

The authors thank Juliette Martin and Nicoletta Ceres for their useful comments on the manuscript.

Author information

Authors and Affiliations

  1. INSERM, UMR-S665, F-75015, Paris, France

    Jonathan Barnoud

  2. Université Paris Diderot, Sorbonne Paris Cité, UMR-S1134, F-75013, Paris, France

    Jonathan Barnoud

  3. CNRS, IBCP (UMR 5086), Lyon, France

    Luca Monticelli

  4. Université Claude Bernard Lyon I, Lyon, France

    Luca Monticelli

Authors
  1. Jonathan Barnoud
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  2. Luca Monticelli
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Corresponding author

Correspondence to Luca Monticelli .

Editor information

Editors and Affiliations

  1. University of Hertfordshire, Hatfield, Hertfordshire, United Kingdom

    Andreas Kukol

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Barnoud, J., Monticelli, L. (2015). Coarse-Grained Force Fields for Molecular Simulations. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods in Molecular Biology, vol 1215. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1465-4_7

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  • DOI: https://doi.org/10.1007/978-1-4939-1465-4_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1464-7

  • Online ISBN: 978-1-4939-1465-4

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