A Practical View of the Martini Force Field

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

*Bijbehorende auteur voor dit werk

OnderzoeksoutputAcademicpeer review

13 Citaten (Scopus)

Samenvatting

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.

Originele taal-2English
Titel Biomolecular Simulations
Subtitel Methods in Molecular Biology
RedacteurenM. Bonomi, C. Camilloni
Plaats van productieHumana, NY
UitgeverijSPRINGER
Pagina's105-127
Aantal pagina's23
ISBN van elektronische versie978-1-4939-9608-7
ISBN van geprinte versie978-1-4939-9607-0
DOI's
StatusPublished - 2019

Publicatie series

NaamMethods in Molecular Biology
Volume2022
ISSN van geprinte versie1064-3745

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