Thickness Analysis
MembraneAnalysis.lipids_thickness_spectrum
— Functionlipids_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 typeLipid
as defined inlipids.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
— Functionpeptide_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 typeLipid
as defined inlipids.jl
;ref_residue
: residue number of the reference residue of the peptide;q_max
: maximum q mode magnitude value to be used.