Forcefield schema
A full description of the overall Forcefield model.
Required Keys
- The following properties are required for the Forcefield specification.
Key Name
Description
Field Type
symbols
An ordered (natom,) list of particle (e.g. atomic elemental) symbols.
array[string]
Optional Keys
- The following keys are optional for the Forcefield specification.
Key Name
Description
Field Type
angles
No description provided.
array[#/definitions/Angles]
atomic_numbers
An optional ordered 1-D array-like object of atomic numbers of shape (nat,). Index matches the 0-indexed indices of all other per-atom settings like
symbols. Values are inferred from thesymbolslist if not explicitly set.array[number]
bonds
No description provided.
array[#/definitions/Bonds]
charge_groups
Charge groups per atom. Length of the array must be natoms.
array[number]
charges
Atomic charges. Default unit is in elementary charge units.
array[number]
charges_units
Atomic charge unit.
string
combination_rule
Combination rule for the force field.
string
comment
Additional comments for this model. Intended for pure human/user consumption and clarity.
string
defs
Particle definition. For atomic forcefields, this could be the atom type (e.g. HH31) or SMIRKS (OFF) representation. The type names are associated with the atomic elements defined in other objects e.g. see the :class:
Moleculemodel.array[string]
dihedrals
No description provided.
array[#/definitions/Dihedrals]
exclusions
Which pairs of bonded atoms to exclude from non-bonded calculations. The rules to apply in choosing bonded exclusions are specifed in the configuration file using the exclude parameter. The choices for exclusions are None, 1-2, 1-3, 1-4, etc. With None, no atom pairs are excluded. With 1-2, only atoms that are connected via a linear bond are excluded. With 1-3, any pair of atoms connected via a bond or bonded to a common third atom are excluded. With 1-4, any atoms that are connected by a linear bond, or a sequence of two bonds, or a sequence of three bonds, are excluded. With scaled1-4, exclusions are applied in the same manner as the 1-3 setting, but those pairs that are connected by a sequence of bonds are calculated using the modified 1-4 methods described rather than the standard force calculations.
string
extras
Additional information to bundle with the object. Use for schema development and scratch space.
object
identifier
Forcefield unique identifier e.g. charmm27, amber99, etc.
string
inclusions
Which pairs of 1-4 excluded bonded atoms to include in non-bonded calculations.
string
masses
List of atomic masses. If not provided, the mass of each atom is inferred from its most common isotope. If this is provided, it must be the same length as
symbols.array[number]
masses_units
Units for atomic masses. Defaults to unified atomic mass unit.
string
name
Common or human-readable name to assign to this model. This field can be arbitrary.
string
nonbonded
No description provided.
array[#/definitions/NonBonded]
provenance
The provenance information about how this object (and its attributes) were generated, provided, and manipulated.
object
schema_name
The MMSchema specification to which this model conforms. Explicitly fixed as mmschema_forcefield.
string
schema_version
The version number of
schema_nameto which this model conforms.integer
substructs
A list of substructure names the particles belong to. E.g. [(‘ALA’, 4), (‘ACE’, 0)] means atom1 belong to residue ALA (alanine) with residue number 4, while atom2 belongs to residue ACE (acetyl) with residue number 0.
array[array]