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.
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Acknowledgements
This work was supported by the School of Life and Medical Sciences, University of Hertfordshire and has made use of the University of Hertfordshire Science and Technology Research Institute high-performance computing facility. I thank all research groups that made their tools and programs available to the research community.
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Kukol, A. (2015). Lipid Membranes for Membrane Proteins. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods in Molecular Biology, vol 1215. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1465-4_4
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DOI: https://doi.org/10.1007/978-1-4939-1465-4_4
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