title: Lipid membranes for membrane proteins.
abstract: The molecular dynamics (MD) simulation of membrane proteins requires the setup of an accurate representation of lipid bilayers. This chapter describes the setup of a lipid bilayer system from scratch using generally available tools, starting with a definition of the lipid molecule POPE, generation of a lipid bilayer, energy minimization, MD simulation, and data analysis. The data analysis includes the calculation of area and volume per lipid, deuterium order parameters, self-diffusion constant, and the electron density profile.
authors.affiliation: School of Life and Medical Sciences, University of Hertfordshire, College Lane, AL10 9AB, Hatfield, Hertfordshire, UK, a.kukol@herts.ac.uk.
authors.forename: Andreas
authors.initials: A
authors.lastname: Kukol
mesh_terms: D000465:Algorithms; D004058:Diffusion; D008051:Lipid Bilayers / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010714:Phosphatidylethanolamines / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D008051:Lipid Bilayers; D008565:Membrane Proteins; D010714:Phosphatidylethanolamines; C057561:1-palmitoyl-2-oleoylphosphatidylethanolamine