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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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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