4.4.1.3. Water: SPC/E

To call this Molecule Type description in , use:

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

4.4.1.3.1. Description

The mean position of the molecule is localised at the Oxygen atom.

4.4.1.3.2. Test performed

TODO

4.4.1.3.3. Module

Frog.Molecules.SPCE.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.SPCE.compute_mean_position(L_pos)

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

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

The electrostatic description of this MT in an explicite PE environement. The same parameters as the MD are used: SPC/E.

Frog.Molecules.SPCE.info_molecule(smparameter)

Basic information for a water MT.

Frog.Molecules.SPCE.info_molecule_for_layer()

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

Frog.Molecules.SPCE.info_molecule_typical_size()

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

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

How to define the molecule in an QM box.

Frog.Molecules.SPCE.typical_geometry()

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