Topology

TopologySchema

Bases: BaseModel, YamlIO

Information that specifies the physical atomistic system.

ff_atom_type = Field(default=None)

In the context of force fields used in molecular dynamics simulations, an "atom type" refers to a specific classification assigned to individual atoms within a molecular system based on certain characteristics. Atom types play a crucial role in defining the parameters and potential energy functions used to calculate forces and motions during a simulation.

Each atom in a molecular system is assigned a particular atom type, which is typically associated with a set of parameters defining its behavior. These parameters include values such as atomic mass, partial charges, van der Waals radii, and bond, angle, and dihedral force constants. The specific values for these parameters are determined based on experimental data and quantum mechanical calculations.

Cadence: ensemble

UUID: e34c0e1b-0eaa-4679-b060-3fcfe737aa15

ids_component = Field(default=None)

Relates ids_entity to a fragment label for chemical components or species. Labels could be WAT or h2o for water, MeOH for methanol, bz for benzene, etc. There are no standardized labels for species.

Cadence: microstate

UUID: cf39af62-d372-4747-a431-cf2fa0c8e119

ids_entity = Field(default=None)

A uniquely identifying integer specifying what atoms belong to which entities. Entities can be a related set of atoms, molecules, or functional group. For example, a water and methanol molecule could be [0, 0, 0, 1, 1, 1, 1, 1, 1].

Cadence: microstate

UUID: b490f2db-548e-4c92-a71a-8222c041ca54