4.4.1.4. Methanol: OPLS/All Atoms

To call this Molecule Type description in , use:

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

4.4.1.4.1. Description

4.4.1.4.2. Test performed

4.4.1.4.3. Module

Frog.Molecules.Methanol_OPLSAA.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.Methanol_OPLSAA.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position.

Frog.Molecules.Methanol_OPLSAA.compute_molecular_orientation(L_pos)

Define how to compute the ‘’molecular orientation’’ of the molecule given its position. The first 3 angles are the projection of the C-O bond in the laboratory axis. The last 3 angles are the projection of the O-H bond in the laboratory axis. WARNING: THIS SHOULD RETURN VALUE BETWEEN -1 AND 1.

Frog.Molecules.Methanol_OPLSAA.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.Methanol_OPLSAA.electrostatic_description(pe_order, electro_neigh, L_pos=False)

Electrostatic description of the Methanol_OPLSAA molecule type. These charges are the same as the usual OPLS/AA force field. The charge are given in e units.

Frog.Molecules.Methanol_OPLSAA.info_molecule(smparameter)

Frog.Molecules.Methanol_OPLSAA.info_molecule_for_layer()

Defines the radii of every atoms for the layer analysis.

Frog.Molecules.Methanol_OPLSAA.info_molecule_typical_size()

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

TODO

Frog.Molecules.Methanol_OPLSAA.typical_geometry()