Fluctuation Analysis

fluctuation_spectrum(;
    pdb_file,
    traj_file,
    output_file,
    lipids,
    ref_atoms=Dict(lipid => lipid.ref_atom for lipid in lipids),
    L_grid)

Calculates the height and thickness fluctuation spectrum of a lipid bilayer simulation trajectory and saves the results as a HDF5 file with labels hq and tq.

Keyword arguments

• pdf_file: PDB structure file;
• traj_file: trajectory file;
• output_file: output HDF5;
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• ref_atoms: a dictionary of reference atoms for each lipid;
• L_grid: length of the lattice grid used to discretize the surface.

area_expansion_modulus(;
    traj_files,
    output_file)

Calculates area expansion modulus in units of kBT per square of length unit in trajectories (e.g., Å^2).

Keyword arguments

• traj_files: a list of trajectory files;
• output_file: output file to save the result.