A Practical View of the MARTINI Force Field

DNA
Book chapter
Protocol
Lipid membranes
Author

Bart MH Bruininks, Paulo CT Souza, Siewert J Marrink

Doi

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

Citation (APA 7)

Bruininks, B. M., Souza, P. C., & Marrink, S. J. (2019). A practical view of the martini force field. Biomolecular Simulations: Methods and Protocols, 105-127.

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.