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.

fluctuation_hq2_data(;
    box_dims,
    fs_files,
    output_file,
    q_max)

Calculates |hq|^2 vs |q| data from fluctuation spectrum. Assumes square (Lx = Ly) bilayer. Saves results to hq2.dat in output_dir.

Keyword arguments

• box_dims: ordered pair of lateral simulation box dimensions, Lx and Ly;
• fs_files: a list of HDF5 fluctuation spectrum files;
• output_dir: output directory;
• q_max: maximum q mode magnitude value to be used.