List of general functions

Contents

Version

2.11

Contact

Please report problems/bugs to michael.holmboe@umu.se

Convert water functions

  1. spc2tip4p(filename) % This function converts a .gro or .pdb file with spc water to some tip4p water
  2. spc2tip5p(filename) % This function converts a .gro or .pdb file with spc water to some tip5p water
  3. spce2tip4p(filename) % This function converts a .gro or .pdb file with spc water to some tip4p water
  4. tip3p2tip4p(filename) % This function converts a .gro file with spc water to some tip4p water

Various distance and bond functions

  1. bond_angle_atom(atom,Box_dim,max_short_dist,max_long_dist,varargin) % This function tries to find all bonds and angles of the atom struct 'more' is an optional varargin argument
  2. bond_angle_dihedral_atom(atom,Box_dim,varargin) % This function tries to find all bonds, angles and dihedrals of the atom struct. Rmaxshort and Rmaxlong as well as 'more' is an optional varargin argument
  3. bond_angle_type(atom1,atom2,Box_dim,rmin,rmax,angle_limit,varargin) % This tries to find all bonds and angles of the atom types
  4. bond_valence_atom(atom,Box_dim,varargin) % This function tries to calculate the bond valence values according to the bond valence method
  5. bond_valence_data(ion1,ion2,R,varargin) % This function fetches the data and matches it to the passed atom types used to calculate the bond valence values according to http://www.iucr.org/resources/data/datasets/bond-valence-parameters
  6. cell_list_dist_matrix_atom(atom,Box_dim,varargin) % This function calculates the distance matrix from the atom struct, using a cell list algorithm adapted from the Matlab MDtoolbox by Yasuhiro Matsunaga
  7. dist_matrix_atom(atom,Box_dim) % This calculates the distance matrix from the atom struct
  8. neigh_atom(atom,Box_dim,rmax,varargin) % This function checks which neighbors each atom has and ouputs their info
  9. neighbor_func(solute_index,XYZ_solute,XYZ_data,Box_dim,radius) % This function scans xyz data and checks who is within a certain radius. It outputs neighbour index,
  10. radius_atom(atom,ffname,watermodel) % This function fetches the ion radius from clayff or interface or interface2015 ff's and
  11. radius_ion(Atom_label) % This function fetches the ionic radius, originally taken from the link below
  12. radius_vdw(Atom_label) % This function fetches the rdw radius, originally taken from below from 'A cartography of the van der Waals territories' Santiago Alvarez doi:10.1039/c3dt50599e
  13. rdf_atom(atom,Box_dim,varargin) % This function calculates the radial distributtion function and the coordination number. Can also do Gaussion smoothing.
  14. xrd_atom(varargin) % This function calculates theoretical XRD patterns from a .pdb|.gro file or from an atom struct and Box_dim.

Other general functions

  1. add2atom(XYZ_labels,XYZ_data,varargin) % This function appends so-called XYZ atomtype labels and XYZ data to an existing atom struct
  2. analyze_atom(atom,Box_dim) % This function fetches various preperties of the atoms in the atom struct, using for instance the bond valence method and for instance the radii originally taken from below Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides. R. D. Shannon Acta Cryst. (1976) A32, 751-767.
  3. atomic_scattering_factors(Atom_label,lambda,twotheta,DW) % This function retrieves the atomic scattering factor vs 2theta using the 11 coeff parameters from Waasmaier Kirfel, 1995
  4. ave_atom(atom) % This function calculates the mean of the atom coordinates
  5. Box_dim2Cell(Box_dim) % * This function transforms the 1x3 or the 1x9 Box_dim variable to the 1x6 Cell variable
  6. cat_atom.m % This is a special script (and not a function) that imports and appends atom structs into a .gro trajectory file, useful to make a trajectory with varying number of particles
  7. Cell2Box_dim(Cell) % This function transforms the 1x6 Cell variable containing the a, b, c cell values and the alfa, beta, gamma angle values as used in a typical .pdb file, into a 1x3 or the 1x9 Box_dim variable
  8. COM_atom(atom,MolID) % This function calculates the COM for certain elements
  9. COM_func(MolID,XYZ_data,Atom_label,XYZ_labels,Box_dim) % This calculates the center of mass for water. Slow due to pbc...
  10. COM_molid(atom,MolID) % This function calculates the COM for certain elements
  11. COM_SOL(MolID,XYZ_data,Atom_label,XYZ_labels,Box_dim) % Computes the COM of SPC water?
  12. composition_atom(atom) % This function looks at the composition of the atom struct
  13. density_atom(atom,Box_dim) % This function calculates concentration and electron density profiles. If the atom struct contains the field charge. the charge density, electric field and electrostatic potential is also calculated.
  14. dipoles_atom(Elements,Box_dim) % This function calculates the dipole vector of water. Similar to the COM_func
  15. draw_box_atom(Box_dim,LineColor,LineThickness) % Draws a box
  16. element_atom(atom,varargin)  % Converts atomtypes to element types. This function replaces the atomtypes names with the element names
  17. element_color(Atom_label) % This function assigns a certain color to each element. Estethic improvements are welcome...
  18. frac2atom(atom,Box_dim,angleparam,angletype) % This function transforms fractional coordinates to cartesian
  19. frame2atom(atom,traj,frame,Box_dim,varargin) % This function extracts a frame to the trajectory matrix
  20. G2_atom(atom,Box_dim) % This function calculates the continuous G2 factor fromthe cos and sin terms and also saves a struct variable for G2_calc_func(). You might wnat to edit the atomtype names below to fit your needs...
  21. hist_atom(atom,s) % This function is used to calculate density profiles in the X|Y|Z-direction
  22. histz_atom(atom,s) % This function is used to calculate density profiles in the Z-direction
  23. molecule_atom(atom,varargin) % This function will set the molecule ID (MolId), residue name (Resname) of the atom struct, ie making the atom struct a single molecule, as well as optionally setting the atomtype names to the resp. elements.
  24. median_atom(atom) % This function calculates the median position of the atom struct
  25. neutralize_atom(atom) % This function appends a 0 to all atomtype names and will also set the charge (if the field charge exist) to zero (0).
  26. orto_atom(atom,Box_dim) % This transforms a triclinic atom struct to an orthogonal atom struct. Box_dim must look like [lx ly lz 0 0 xy 0 xz yz]
  27. PATH2<gmx() % The Gromacs path on your computer
  28. PATH2VMD() % The VMD path on your computer
  29. place_atom(atom,position) % This function places the atom struct according to the position vector called position, trying to use the COM of the molecule
  30. plot_density_atom(atom,Box_dim,varargin) % This function draws the atom struct in 3D adjoined by some density profiles
  31. plot_atom(atom,Box_dim,varargin) % This function draws the atom struct in 3D. Its very simplistic with no cool features
  32. reduced_mass(Atom_label1,varargin) % This function calculates the reduced mass.
  33. show_density_atom(atom,Box_dim,varargin) % This function draws the atom struct in 3D adjoined by some density profiles
  34. show_atom(atom,varargin) % This function draws the atom struct in 3D. Its a bit fancier that plot_atom()
  35. show_arrow(p1,p2,varargin) % * plot a 3D arrow as patch object (cylinder+cone). This function was adapted from mArrow3.m
  36. show_axis(varargin) % * This function draws the axis in a plot
  37. show_box(Box_dim) % * This function draws the simulation box
  38. show_miller(Box_dim) % * This function draws the hkl Miller planes of the Box_dim/Cell variables
  39. triclinic_atom(atom,Box_dim,angleparam,angletype) %  triclinic_atom.m - This transforms an orthogonal atom struct to a triclinic with the angles alfa, beta, gamma or tilt factors xy, xz, yz
  40. update_atom(atom) % This function updates the molid index and the atoms index in the atom struct
  41. vmd(atom,Box_dim) % This function plots the atom struct

Keep/remove functions

  1. keep_atom(atom,resname) % keep_atom.m - This removes all but resname
  2. keep_resname(atom,resnames) % keep_resname.m - This removes all but the resnames
  3. remove_molid(atom,MolID) %  remove_molid.m - This removes residue with molid MolID = [1 2 3 .....]
  4. remove_occypancy_atom(atom) % This function removes all succeding particles in the atom struct that has identical coordinates to a preceding particle
  5. remove_residues(atom,resnames,lo,hi,dim) % This function section is used to remove residues in the simulation box between limits lo and hi
  6. remove_resname(atom,resnames) % This function removes residue with molid MolID, resnames = {'SOL' 'Protein'}
  7. remove_SOL(atom,atomname,lo,hi,dim) %  This section is used to remove residues in the simulation box between limits lo and hi
  8. remove_type(atom,typescell) % This function removes atomtypes with types as in typescell = {'OW' 'HW1' 'HW2'}


Published with MATLAB® R2022a