Thickness Analysis

MembraneAnalysis.lipids_thickness_spectrum — Function
lipids_thickness_spectrum(;
    pdb_file,
    traj_files,
    fs_files,
    output_dir,
    lipids,
    ref_atoms=Dict(lipid => lipid.ref_atom for lipid in lipids),
    q_max)

Calculates thickness spectrum of the lipids using their reference atom position. Assumes square (Lx = Ly) bilayer. Results for lipid "XXXX" will be stored in XXXX_tqs.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.
MembraneAnalysis.peptide_thickness_spectrum — Function
peptide_thickness_spectrum(;
    pdb_file,
    traj_files,
    fs_files,
    output_file,
    lipids,
    ref_residue),
    q_max)

Calculates thickness 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.