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Biomolecular Simulations pp 105–127Cite as

A Practical View of the Martini Force Field

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2022))

Abstract

Martini is a coarse-grained (CG) force field suitable for molecular dynamics (MD) simulations of (bio)molecular systems. It is based on mapping of two to four heavy atoms to one CG particle. The effective interactions between the CG particles are parametrized to reproduce partitioning free energies of small chemical compounds between polar and apolar phases. In this chapter, a summary of the key elements of this CG force field is presented, followed by an example of practical application: a lipoplex-membrane fusion experiment. Formulated as hands-on practice, this chapter contains guidelines to build CG models of important biological systems, such as asymmetric bilayers and double-stranded DNA. Finally, a series of notes containing useful information, limitations, and tips are described in the last section.

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Acknowledgments

The authors would like to thank the many people who have directly and indirectly contributed to the development of the Martini force field. In particular Alex de Vries, Helgi I. Ingolfsson, Manuel N. Melo, Tsjerk Wassenaar, Xavier Periole and all the past and present members of the MD group in Groningen, as well as the many users abroad, are acknowledged for their dynamism and enthusiasm in using, criticizing, and improving Martini.

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Authors and Affiliations

  1. Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands

    Bart M. H. Bruininks, Paulo C. T. Souza & Siewert J. Marrink

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  1. Bart M. H. Bruininks
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  2. Paulo C. T. Souza
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  3. Siewert J. Marrink
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Correspondence to Siewert J. Marrink .

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Editors and Affiliations

  1. Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France

    Massimiliano Bonomi

  2. Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

    Carlo Camilloni

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Bruininks, B.M.H., Souza, P.C.T., Marrink, S.J. (2019). A Practical View of the Martini Force Field. In: Bonomi, M., Camilloni, C. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 2022. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9608-7_5

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  • DOI: https://doi.org/10.1007/978-1-4939-9608-7_5

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  • Publisher Name: Humana, New York, NY

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