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mbuild_bilayer

A bilayer building plugin for mBuild.

Usage: mbuild.recipes.Bilayer():

Arguments:

lipids : list

List of tuples in format (lipid, frac) where frac is the fraction of that lipid in the bilayer (lipid is a Compound)
ref_atoms : int

Indices of the atom in lipids to form the interface, one for each lipid in lipids (i.e., this atom is shifted to the 'interface' level)
n_lipids_x : int

Number of lipids in the x-direction per layer.
n_lipids_y : int

Number of lipids in the y-direction per layer.
area_per_lipid : float

Area per lipid.
solvent : Compound

Compound to solvate the bilayer with. Typically, a pre-equilibrated box of solvent.
lipid_box : mb.Box, optional

A mb.Box containing the lipids where no solvent will be added.
spacing_z : float, optional

Amount of space to add between opposing monolayers.
solvent_per_lipid : int, optional, default=None

Number of solvent molecules per lipid
n_solvent : int, optional, default=None

Total number of solvent molecules.
tilt: float, optional, default=None

Tilt angle relative to the bilayer normal to prescribe to lipids. Units are radians.
random_seed : int, optional, default=12345

Seed for random number generator for filling in lipids.
mirror : bool, optional, default=True

Make top and bottom layers mirrors of each other.