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.

Copyright

Copyright (c) 2019, Parashara Shamaprasad and Tim Moore

Acknowledgements

Project based on the mBuild Recipe Cookiecutter