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Building complex membranes with Martini 3.
Ozturk, Tugba Nur; König, Melanie; Carpenter, Timothy S; Pedersen, Kasper B; Wassenaar, Tsjerk A; Ingólfsson, Helgi I; Marrink, Siewert J.
Affiliation
  • Ozturk TN; Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
  • König M; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
  • Carpenter TS; Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
  • Pedersen KB; Department of Chemistry, Aarhus University, Aarhus C, Denmark.
  • Wassenaar TA; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands; Institute for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands.
  • Ingólfsson HI; Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States. Electronic address: ingolfsson1@llnl.gov.
  • Marrink SJ; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands. Electronic address: s.j.marrink@rug.nl.
Methods Enzymol ; 701: 237-285, 2024.
Article in En | MEDLINE | ID: mdl-39025573
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Molecular Dynamics Simulation / Lipid Bilayers / Membrane Proteins Language: En Journal: Methods Enzymol Year: 2024 Type: Article Affiliation country: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Molecular Dynamics Simulation / Lipid Bilayers / Membrane Proteins Language: En Journal: Methods Enzymol Year: 2024 Type: Article Affiliation country: United States