Building complex membranes with Martini 3

Tugba Nur Ozturk; Melanie König; Timothy S. Carpenter; Kasper B. Pedersen; Tsjerk A. Wassenaar; Helgi I. Ingólfsson; Siewert J. Marrink

doi:10.1016/bs.mie.2024.03.010

Building complex membranes with Martini 3

Tugba Nur Ozturk, Melanie König, Timothy S. Carpenter, Kasper B. Pedersen, Tsjerk A. Wassenaar, Helgi I. Ingólfsson^*, Siewert J. Marrink^*

^*Corresponding author for this work

Molecular Dynamics

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Abstract

The Martini model is a popular force field for coarse-grained simulations. Membranes have always been at the center of its development, with the latest version, Martini 3, showing great promise in capturing more and more realistic behavior. In this chapter we provide a step-by-step tutorial on how to construct starting configurations, run initial simulations and perform dedicated analysis for membrane-based systems of increasing complexity, including leaflet asymmetry, curvature gradients and embedding of membrane proteins.

Original language	English
Pages (from-to)	237-285
Number of pages	49
Journal	Methods in Enzymology
Volume	701
Early online date	9-Apr-2024
DOIs	https://doi.org/10.1016/bs.mie.2024.03.010
Publication status	Published - Jul-2024

Keywords

Asymmetrical membranes
Complex membranes
Curved membranes
Embedding proteins in membranes
Leaflet asymmetry
Martini 3
Membrane set up

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10.1016/bs.mie.2024.03.010

Building complex membranes with Martini 3Final publisher's version, 4.75 MBLicence: Taverne

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title = "Building complex membranes with Martini 3",

abstract = "The Martini model is a popular force field for coarse-grained simulations. Membranes have always been at the center of its development, with the latest version, Martini 3, showing great promise in capturing more and more realistic behavior. In this chapter we provide a step-by-step tutorial on how to construct starting configurations, run initial simulations and perform dedicated analysis for membrane-based systems of increasing complexity, including leaflet asymmetry, curvature gradients and embedding of membrane proteins.",

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doi = "10.1016/bs.mie.2024.03.010",

language = "English",

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AU - Ozturk, Tugba Nur

AU - König, Melanie

AU - Carpenter, Timothy S.

AU - Pedersen, Kasper B.

AU - Wassenaar, Tsjerk A.

AU - Ingólfsson, Helgi I.

AU - Marrink, Siewert J.

PY - 2024/7

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AB - The Martini model is a popular force field for coarse-grained simulations. Membranes have always been at the center of its development, with the latest version, Martini 3, showing great promise in capturing more and more realistic behavior. In this chapter we provide a step-by-step tutorial on how to construct starting configurations, run initial simulations and perform dedicated analysis for membrane-based systems of increasing complexity, including leaflet asymmetry, curvature gradients and embedding of membrane proteins.

KW - Asymmetrical membranes

KW - Complex membranes

KW - Curved membranes

KW - Embedding proteins in membranes

KW - Leaflet asymmetry

KW - Martini 3

KW - Membrane set up

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SN - 0076-6879

VL - 701

SP - 237

EP - 285

JO - Methods in Enzymology

JF - Methods in Enzymology

ER -

Building complex membranes with Martini 3

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Keywords

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