4.4.1.2. Water: TIP4P2005 - O

To call this Molecule Type description in , use:

myMT = frog_class.MoleculeType(GP, 'Water_TIP4P2005_O', where_are_molecules)

Note

If you want to do the same little variation on a Molecule Type description (like changing the ‘mean position’ localisation or ‘molecular orientation’, just copy past the original library file, change the name an the function desired. You have to recompile the code in order to update the path so that can find where is located the new file. See here for more details.

4.4.1.2.1. Description

The mean position of the molecule is localised in the Oxygen position.

4.4.1.2.2. Test performed

4.4.1.2.3. Module

Frog.Molecules.Water_TIP4P2005.compute_hbonds(L_target, name_partner, L_partner, parameter, info=False)

Define how to compute the ‘’hbonds’’ of this molecule type with a partner molecule type. The definition should depend on the partner molecule.

Frog.Molecules.Water_TIP4P2005.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position. Here at the ‘negative charge’ position.

Frog.Molecules.Water_TIP4P2005.compute_molecular_orientation(L_pos)

Define how to compute the ‘’molecular orientation’’ of the molecule given its position. Here its the projection of the dipole moment on the laboratory axis. WARNING: THIS SHOULD RETURN VALUE BETWEEN -1 AND 1.

Frog.Molecules.Water_TIP4P2005.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Water_TIP4P2005.electrostatic_description(pe_level, electro_description, L_pos=False)

How to represent this molecule in an explicite electrostatic environement. The same electrostatic parameters are used as in the MD. The negative charge IS NOT at the oxygen position but at localisation X. The positive charge are at the Hydrogen positions.

Frog.Molecules.Water_TIP4P2005.info_molecule(smparameter)

Basic information for a water MT.

Frog.Molecules.Water_TIP4P2005.info_molecule_for_layer()

Defines the radii of every atoms for the layer analysis. These value are used by the pytim module.

Frog.Molecules.Water_TIP4P2005.info_molecule_typical_size()

This function is not ‘mandatory’. It is used within info_molecule.

Frog.Molecules.Water_TIP4P2005.qm_target_description(qmparameter, qmdescription, L_pos=False)

How to define the molecule in an QM box.

Frog.Molecules.Water_TIP4P2005.test_electrostatic(electro_neigh, L_pos=False)

An example of a very complex electrostatic description

Frog.Molecules.Water_TIP4P2005.typical_geometry()

Defines a typical geometry of this molecule. Should return a 3D numpy array.