CDTK.gmx2cdtk module
This module has several functions to transform coordinates and velocities obtained
from Gromacs calculation into suitable input files for CDTK. Use gmx2cdtk -h
to find out how to use this program.
Basic units in GMX, please look at the following web. https://manual.gromacs.org/documentation/2019/reference-manual/definitions.html#table-basicunits
1 Picoseconds = 41341.374575751 Atomic Unit Of Time 1 nm = 18.8973 Bohr 1 nm/ps = 18.8973/41341.374575751 Bohr/a.u. = 0.00045710381413114194 1 nm/ps = 4.571038E-04 Bohr/a.u.
- CDTK.gmx2cdtk.atomName2Element(atomName)[source]
converts atomName into element name :param atomName: :type atomName: string
- Returns:
element name
- Return type:
string
- CDTK.gmx2cdtk.atomName2atomMass(atomName)[source]
converts atomName into element mass :param atomName: :type atomName: string
- Returns:
element mass in atomic units
- Return type:
float
- CDTK.gmx2cdtk.atomName2atomNum(atomName)[source]
converts atomName into element number :param atomName: :type atomName: string
- Returns:
element number
- Return type:
index
- CDTK.gmx2cdtk.get_coord_center(n_center, molec, centerMethod='first')[source]
This will return the coordinate center of residue index n_center
- Parameters:
Ncenter (int) – Index of molecule (residue index) that you want to be the center.
molec (dict of ndarrays.)
centerMethod (either "com" or "first")
- Returns:
X, Y, Z coordinates of center.
- Return type:
ndarray of float.
- CDTK.gmx2cdtk.makeResiduesWhole(molec)[source]
Rearranges the atoms by multiples of boxsize such that the residues are closest together
- Parameters:
molec (dict of ndarray.)
- Returns:
xyz – new coordinates.
- Return type:
(n_atoms, 3) ndarray of float.
- CDTK.gmx2cdtk.print_geom_files(molec)[source]
Prints input files needed for xsample first sorting all atoms from closest to the center of the box to furthest. The files printed are .in, .xyz and .vel.
- Parameters:
molec (dict of ndarray.) – Dictionary built from reading gromax file (check readgmx documentation).
- CDTK.gmx2cdtk.readgmx(filename, check_water=False)[source]
Read gromacs file and return the topolgy, element types, coordinates, velocities of all atoms and the box size.
- Parameters:
filename (string) – Name of gromacs file.
- Returns:
molec – Dictionary containing the following arrays: - geom : (n_atoms, 3) ndarray of float.
Coordinates of all atoms.
- vel(n_atoms, 3) ndarray of float.
Velocities of all atoms.
residueIndex: (n_atoms) ndarray of ints
residueName: (n_atoms) ndarray of str
- topol(n_atoms) ndarray of str.
String identifiers for the topology of the system (atoms in molecules).
- atomlist(n_atoms) ndarray of str.
String identifiers of all atoms types (e.g., “O”, “H”).
- atomnums(n_atoms) ndarray of int.
Intigers with atomic numners of each element in atomloist.
- atommass(n_atoms) ndarray of float.
Atomic masses of each element in atomlist.
- boxsize(3) ndarray of float.
Box size (len_x, len_y, len_z).
- residueName(n_atoms) ndarray of str
Name of residue for each atom
- residueIndex(n_atoms) ndarray of int
Index of residue for each atom
- atomName(n_atoms) ndarray of str
Name of atoms (e.g. “OW”, “HW1”)
- Return type:
dict of ndarray.
- CDTK.gmx2cdtk.shift_box(shift, xyz, v_box)[source]
Shift all molecules by shift and move atoms that fall outside the box according to periodic boundary conditions :param shift: X, Y, Z coordinates of new center (oxygen atom). :type shift: (3) ndarray of float. :param xyz: Original coordinates of all atoms. :type xyz: (n_atoms, 3) ndarray of float.
- Returns:
New coordinates centered arund center_new in the box.
- Return type:
(n_atoms, 3) ndarray of float.
- CDTK.gmx2cdtk.sort_molec(molec, skipDistance=False)[source]
Sorts the molecules (residues) according to their center-of-mass positions (distance to the origin)
- Parameters:
molec (dict of ndarray.) – Dictionary built from reading gromax file (check readgmx documentation).
- Returns:
molec – Updated dictionary with sorted molecules.
- Return type:
dict of ndarray
- CDTK.gmx2cdtk.writegmx(filename, molec, reIndexResidues=True)[source]
Writes gromacs .gro file from molec stricture
- Parameters:
filename (string) – Name of gromacs file.
molec (dict of ndarray.) –
Dictionary containing the following arrays: - geom : (n_atoms, 3) ndarray of float.
Coordinates of all atoms.
- vel(n_atoms, 3) ndarray of float.
Velocities of all atoms.
- topol(n_atoms) ndarray of str.
String identifiers for the topology of the system (atoms in molecules).
- atomlist(n_atoms) ndarray of str.
String identifiers of all atoms types.
- atomnums(n_atoms) ndarray of int.
Intigers with atomic numners of each element in atomloist.
- atommass(n_atoms) ndarray of float.
Atomic masses of each element in atomlist.
- boxsize(3) ndarray of float.
Box size (len_x, len_y, len_z).
- residueName(n_atoms) ndarray of str
Name of residue for each atom
- residueIndex(n_atoms) ndarray of int
Index of residue for each atom
- atomName(n_atoms) ndarray of str
Name of atoms (e.g. “OW”, “HW1”)