4.3. Single Molecule Parameter

This object is fully defined in the molecular library file attached to the MT. More informations about how to construct these quantity using the molecular library file are provided HERE.

It is important to be coherent between the topology of the MD and the single molecule parameter: since does not read the atom type name from the topology, you may have a case where there is no error due to geometrical mismatch, but the atomic assignation are wrong. Therefore, take some time to open your MD and to check that the 2 description matches.

If there is a difference of description, you can either redo your MD with the same description, or modify the molecular library file.

The single molecule parameter object contains:

SingleMoleculeParameter.name_mt

Type [str]

The name of the MT used to defined this ensemble. Should be the same as the libreary molecular file and the MT.

SingleMoleculeParameter.nbr_atom

Type [int]

The number of atom of this molecule type.

Example

For water, if the MD provides the atom position set nbr_atom to 3.

If the MD provides also the position of the dipole, you should set as many ‘atom’ as position stored in the MD trajectory – so maybe 4.

SingleMoleculeParameter.L_type_atom

Type [list]

The list of atom. The size of L_type_atom should be equal to nbr_atom.

Note

The list can be completly different from the labelling of the MD. This labelling is used for user-friendly prints only.

Note

The name can de different from the one of qm_target_description and electrostatic_description.

SingleMoleculeParameter.size_typical_molecule

Type [float]

A typical value of the size of the molecule. The idea is to help Frog to reconstruct the geometry of the molecule is PBC condition are applied. If also help Frog to find neighborgs.

Example

For water, you can set size_typical_molecule to 2 Angstrom.

SingleMoleculeParameter.max_distance_atom

Type [list]

Defines maximal distance for every atom with respect to a ‘’reference’’ atom. The aim is to help Frog to deal with ‘cutted’ molecule due to PBC condition.

This value should be a list: [The ‘’reference’’ atom, Value for atom 0, Value for atom 1, …].

Where “Value for atom 0” should be ‘Ref’ or the maximal distance allowed from the ‘’reference’’ atom. Note that the atom numerotation starts from 0. If one atom of a molecular trajectory does not respect this maximal distance from the reference atom, Frog tries to move it using the box size of the MD simulation at the given time step. Thus, it is important to be strict enough with respect to these distance – being too restrictive will lead to crashes (with error message) if Frog fails to respect these conditions.

Example

For water, L_type_atom = [O, H, H], one can set:

max_distance_atom = [0, ‘Ref’, 2, 2]

The Oxygen atom is the reference atom, and the Hydrogens should not be more away from it then 2 Angstrom.

SingleMoleculeParameter.d_molecular_orientation

Type [int]

The number of number needed to defined the ‘orientation’ of the molecule in the laboratoy frame. You can go from 1 to N.

Example

For the water molecule, you can define the orientation using 3 ‘angles’.

For more complexe molecule, you can use many more ‘angles’.