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 (Ų) 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: