.. _config_ref tasks make_membrane_system bilayer:

``bilayer``
===========

Parameters controlling bilayer generation

Single-valued attributes:

  * ``lipids``: declaration of lipids in each leaflet in memgen format LIP1[:LIP2][//LIP3] where ":" is an intra-leaflet separator and "//" is an inter-leaflet separator (default: POPC)

  * ``lipid_conformers``: declaration of which conformer index to use for each lipid in memgen format C1:C2//C3 (defaults to 0); must be congruent with the lipids attribute (default: 0)

  * ``mole_fractions``: declaration of mole fractions of each lipid in each leaflet in memgen format R1:R2//R3; must be congruent with the lipids attribute (default: 1.0)

  * ``half_mid_zgap``: extra gap between hydrophobic tails in bilayer during packing, Angstroms (default: 1.0)

  * ``solvents``: string in memgen format SOL1:SOL2:... (default: TIP3)

  * ``solvent_mole_fractions``: string in memgen format x_1:x_2:... (default: 1.0)

  * ``solvent_to_lipid_ratio``: ratio of solvent molecules to lipids in each leaflet; must be specified if solvents are present (default: 32.0)

  * ``SAPL``: estimate of surface area per lipid (Å²) for building initial patches (default: 75.0)

  * ``dims``: box dimensions in x, y, and z in Å; must be specified for a bilayer-only system

  * ``npatch``: box dimensions in number of patches in x and y

  * ``solution_gcc``: solution density in g/cc (default: 1.0)

  * ``cation``: name of salt cation (default: POT)

  * ``anion``: name of salt anion (default: CLA)

  * ``salt_con``: salt concentration in M

  * ``nloop``: number of packmol GENCAN loops for every component

  * ``nloop_all``: number of packmol GENCAN loops for altogether packing

  * ``tolerance``: clash detection tolerance for packmol

  * ``seed``: RNG seed (optional)



Subattributes:

.. toctree::
   :maxdepth: 1

   bilayer/prebuilt
   bilayer/patch_nlipids
   bilayer/composition
   bilayer/relaxation_protocols


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