Analysis

bilayer_analysis_functions.py

Analysis functions for basic bilayer structural properties (APL, APT, tilt, offsets, S2, interdigitation, density profiles, height)

grid_analysis.py

Functions to grid-up and analyzel leaflets, used with permeability calculations

interfacial_roughness.py

Functions to analyze the roughness of the bilayer/water interface

group_templates.py

Contains information about head groups and tail groups for different lipid molecules, depending on the forcefield used

visualize_curvature.py

Use matplotlib to animate the Z-coordinates of lipids over the course of a simulation

bootstrap_perm_pickle.py

Utilize a bootstrapping methodology for Z-constrained simulations to resample force timeseries and compute diffusion, free energy, and permeability

naive_perm_pickle.py

Utilize a naive statistical sampling for Z-constrained simulations to resample force timeseries and compute diffusion, free energy, and permeability