density_distribution

func_membrane_center_z(universe, lipid_resnames) → float

Calculate center of mass of all lipid atoms along z-axis.

paramuniverse

paramlipid_resnameslist[str]

Returns

float

func_density_distribution_frame(atomgroup, lipid_map, water_list, bins, z_centers) → list[dict[str, float | int | str]]

paramatomgroup

paramlipid_map

paramwater_list

parambins

paramz_centers

Returns

list[dict[str, float | int | str]]

funcdensity_distribution(simulation, *, start_ns=0.0, end_ns=None, last_ns=None, stride=1, bin_width=1.0, backend='multiprocessing', n_workers=4) → pd.DataFrame

Compute z-density distributions for lipid head/tail atoms and water.

paramsimulationSimulation

Simulation instance with universe and build input.

paramstart_nsfloat | None

= 0.0

Start time for analysis (ns). Use None to start at frame 0. Ignored when last_ns is set.

paramend_nsfloat | None

= None

End time for analysis (ns). Use None for end of trajectory.

paramlast_nsfloat | None

= None

Analyze the last N ns of the trajectory. Overrides start_ns.

paramstrideint

= 1

Frame stride.

parambin_widthfloat

= 1.0

Bin width in Angstrom.

parambackendstr

= 'multiprocessing'

MDAnalysis backend for parallel execution.

paramn_workersint

= 4

Number of workers for parallel execution.

Returns

pandas.DataFrame

Columns: time_ns, frame, z, density_percent, species, group.