Curvature Analysis

curvature(;
    point,
    hq,
    box_dims,
    q_max,
    q_min=0)

Calculates curvature per mode of a point from fluctuation spectrum.

Keyword arguments

• point: ordered pair of X and Y values;
• hq: 2D matrix of height fluctuation spectrum;
• box_dims: ordered pair of simulation box Lx and Ly values;
• q_max: maximum q mode magnitude value to be used.
• q_min: minimum q mode magnitude value to be used (zero by default).

lipids_sampled_curvature(;
    pdb_file,
    traj_files,
    fs_files,
    output_dir,
    lipids,
    q_max,
    q_min=0)

Calculates mean sampled curvature of heavy atoms of each lipid. Results for lipid "XXXX" will be stored in XXXX_cs.dat in the output directory.

Keyword arguments

• pdb_file: PDB structure file;
• traj_files: a list of trajectory files;
• fs_files: a list of corresponding HDF5 fluctuation spectrum files of the trajectory files;
• output_dir: output directory;
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• q_max: maximum q mode magnitude value to be used.
• q_min: minimum q mode magnitude value to be used (zero bu default).

peptide_sampled_curvature(;
    pdb_file,
    traj_files,
    fs_files,
    output_dir,
    lipids,
    q_max)

Calculates mean sampled curvature of CA atoms of peptide residues.

Keyword arguments

• pdb_file: PDB structure file;
• traj_files: a list of trajectory files;
• fs_files: a list of corresponding HDF5 fluctuation spectrum files of the trajectory files;
• output_file: output file;
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• n_residues: number of residues in the peptide;
• q_max: maximum q mode magnitude value to be used.

lipids_curvature_spectrum(;
    pdb_file,
    traj_files,
    fs_files,
    output_dir,
    lipids,
    ref_atoms=Dict(lipid => lipid.ref_atom for lipid in lipids),
    q_max,
    q_min,
    nqs)

Calculates curvature spectrum of the lipids using their reference atom position. Assumes square (Lx = Ly) bilayer. Results for lipid "XXXX" will be stored in XXXX_cqs.dat in the output directory.

Keyword arguments

• pdb_file: PDB structure file;
• traj_files: a list of trajectory files;
• fs_files: a list of corresponding HDF5 fluctuation spectrum files of the trajectory files;
• output_dir: output directory;
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• ref_atoms: a dictionary of reference atoms for each lipid;
• q_max: maximum q mode magnitude value to be used;
• q_min: minimum q mode magnitude value to be used;
• nqs: number of segments to divide the q range from qmin to qmax;
• tag_files: a list of corresponding lipid interaction tag files of the trajectory files. Uses all lipids by default;
• tag_id: the tag id of the selected lipids.

peptide_curvature_spectrum(;
    pdb_file,
    traj_files,
    fs_files,
    output_file,
    lipids,
    ref_residue),
    q_max)

Calculates curvature spectrum of the peptide using the CA atom of its reference residue. Assumes square (Lx = Ly) bilayer.

Keyword arguments

• pdb_file: PDB structure file;
• traj_files: a list of trajectory files;
• fs_files: a list of corresponding HDF5 fluctuation spectrum files of the trajectory files;
• output_file: output file;
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• ref_residue: residue number of the reference residue of the peptide;
• q_max: maximum q mode magnitude value to be used.

TCB_analysis(;
    input_dir,
    lipids,
    weights=ones(length(lipids)) ./ length(lipids),
    z_cutoff,
    area=readdlm(input_dir * "A.dat")[1],
    output_dir,
    tcb_plot=false)

Calculates bilayer bending rigidity modulus and mean sampled curvature of lipids relative to a weighted average from transverse curvature bias analysis. Optionally plots mean sampled curvature of atoms of each lipid as a function of height.

Keyword arguments

• input_dir: directory with lipid atoms height and curvature files (e.g. XXXX_zs.dat and XXXX_cs.dat for lipid "XXXX");
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• weights: a list of the same size as lipids, determining the weight of each lipid's TCB curve in the analysis. (Should be equal to the fraction of bilayer area covered by that lipid. Will be equal by default.);
• z_cutoff: cutoff height to exclude anomalous behavior near lipid head region;
• area: bilayer area, will be read from A.dat in input_dir by default;
• output_dir: output directory;
• tcb_plot: saves a plot (TCB_plot.pdf) in output_dir if true.

hq2_analysis(;
    input_dir,
    n_points=size(readdlm(input_dir * "hq2.dat"))[1],
    area=readdlm(input_dir * "A.dat")[1],
    model="TD",
    output_dir,
    hq2_plot=false)

Calculates bilayer bending rigidity modulus by fitting |q|^4 × <|hq|^2> vs |q| data to the chosen model. Available models are "HC" (Helfrich-Canham), "MNK" (May-Narang-Kopelevich), or "TD" (Terzi-Deserno), as denoted by equations (36), (37), and (47) respectively in the following paper:

https://doi.org/10.1063/1.4990404

Saves the results to kc_hq2.dat in output_dir and optionally plots the fit.

Keyword arguments

• input_dir: input directory containing hq2.dat;
• n_points: number of |q| data points to use (uses all by default);
• model: chosen theoretical model to fit <|hq|^2> vs |q|;
• area: bilayer area, will be read from A.dat in input_dir by default;
• output_dir: output directory;
• hq2_plot: saves a plot (hq2_plot.pdf) in output_dir if true.