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To run an MD simulation in a Membrane.

• Convert your protein to an ICM object.
• MolMechanics/Run MD Simulation - Click on the Membrane tab.
• Select a region of your protein around which you wish to center the membrane. It implements a basic membrane embedding using a pre-built lipid bilayer (~95x95Å POPE/POPC mix).
• You can choose the option to perform embedding of the membrane before the simulation starts which will make sure all waters are all removed from the membrane before the main simulation begins.

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