Density Analysis

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

Calculates lateral density (number per cell) spectrum of lipids in a lipid bilayer simulation trajectory and saves the results as a HDF5 file with labels XXXX_1 and XXXX_2 for lipid "XXXX" in the two leaflets.

Keyword arguments

• pdf_file: PDB structure file;
• traj_file: trajectory file;
• fs_file: flucuation spectrum 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.

peptide_density_spectrum(;
    pdb_file,
    traj_file,
    fs_file,
    output_file,
    lipids,
    ref_residue,
    L_grid)

Calculates lateral density (number per cell) spectrum of the peptide using the CA atom of its reference residue and saves the results as a HDF5 file with labels PEP_1 and PEP_2 for the two leaflets.

Keyword arguments

• pdf_file: PDB structure file;
• traj_file: trajectory file;
• fs_file: flucuation spectrum file;
• output_file: output HDF5;
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• ref_residue: residue number of the reference residue of the peptide;
• L_grid: length of the lattice grid used to discretize the surface.

lipids_radial_distribution(;
    pdb_file,
    traj_file,
    fs_file,
    output_file,
    lipids,
    ref_atoms=Dict(lipid => lipid.ref_atom for lipid in lipids),
    lipid_A,
    lipid_B,
    max_r=20,
    n_bins=200,
    same_leaflet=true)

Calculates the lateral (2-D) radial density function of lipid A and lipid B in a lipid bilayer simulation trajectory.

Keyword arguments

• pdf_file: PDB structure file;
• traj_file: trajectory file;
• fs_file: flucuation spectrum file;
• output_file: output file (density as a function of histogram bin center);
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• ref_atoms: a dictionary of reference atoms for each lipid;
• lipid_A: the lipid distance is measured from;
• lipid_B: the lipid distance is measured to;
• max_r: maxumum radius (20 by default);
• n_bins: number of histogram bins (200 by default);
• same_leaflet: calculate RDF between lipids in the same leaflet (apposing leaflet if false).

lipids_radial_distribution(;
    pdb_file,
    traj_file,
    fs_file,
    output_file,
    lipids,
    ref_atoms=Dict(lipid => lipid.ref_atom for lipid in lipids),
    ref_residue,
    lipid,
    max_r=20,
    n_bins=200,
    same_leaflet=true)

Calculates the lateral (2-D) radial density function of peptide and a lipid in a lipid bilayer simulation trajectory.

Keyword arguments

• pdf_file: PDB structure file;
• traj_file: trajectory file;
• fs_file: flucuation spectrum file;
• output_file: output file (density as a function of histogram bin center);
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• ref_atoms: a dictionary of reference atoms for each lipid;
• ref_residue: residue number of the reference residue of the peptide;
• lipid: the lipid distance is measured to;
• max_r: maxumum radius (20 by default);
• n_bins: number of histogram bins (200 by default);
• same_leaflet: calculate RDF between lipids in the same leaflet (apposing leaflet if false).