A Practical View of the Martini Force Field

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

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

13 Citations (Scopus)

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.

Original languageEnglish
Title of host publication Biomolecular Simulations
Subtitle of host publication Methods in Molecular Biology
EditorsM. Bonomi, C. Camilloni
Place of PublicationHumana, NY
PublisherSPRINGER
Pages105-127
Number of pages23
ISBN (Electronic)978-1-4939-9608-7
ISBN (Print)978-1-4939-9607-0
DOIs
Publication statusPublished - 2019

Publication series

NameMethods in Molecular Biology
Volume2022
ISSN (Print)1064-3745

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