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Made with VMD
Biological membranes are complex assemblies of diverse lipids, and molecular dynamics (MD) simulation has been among the most effective biophysical tools to investigate them at an atomic-detailed level. Nevertheless, capturing the wide range of lipid compositions and their mixing continues to pose a major challenge to simulations, due to the very slow diffusion of lipids. This issue is particularly important when membrane proteins are present in the membrane and one is interested in studying how they interact with lipids. One solution to partially address this problem is to randomize the initial configuration of lipids in replicate simulations. The Center has developed a toolkit to rapidly clone a membrane with a specific lipid composition into as many copies (with shuffled lipids) as needed within a matter of minutes. The Membrane Mixer Plugin (MMP) uses advanced features in NAMD to remove clashes and make room before shuffling the lipids; it also performs several checks to test the quality of the generated membranes. This method can be accessed via a user-friendly GUI interface in the latest version of VMD.