parametrize | MDFactory

Force field parametrization for molecular species.

attributeparameter_set_types

= {'gromacs': GromacsSingleMoleculeParameterSet}

attributeDISPATCH_ENGINE_PARAMETRIZE

= {'gromacs': {'cgenff': parametrize_cgenff_gromacs, 'smirnoff': parametrize_smirnoff_gromacs}}

attributeDISPATCH_TOPOLOGY_BUILD

= {'gromacs': generate_gromacs_topology}

func_replace_moleculetype(itp_path, new_name) → None

paramitp_pathPath

paramnew_namestr

Returns

None

func_extract_defaults_block(top_path) → str

paramtop_pathPath

Returns

str

func_build_smirnoff_parameter_itp(top_path, atomtypes_path, out_path) → None

paramtop_pathPath

paramatomtypes_pathPath

paramout_pathPath

Returns

None

funcretrieve_or_deposit_parameters(engine, parametrization)

Return a decorator that caches parametrization results in the local parameter store.

paramenginestr

Simulation engine (e.g., "gromacs")

paramparametrizationstr

Force field scheme (e.g., "cgenff", "smirnoff")

Returns

None

funcparametrize_cgenff_gromacs(species) → GromacsSingleMoleculeParameterSet

Parametrize a species using CGenFF for GROMACS.

paramspeciesSingleMoleculeSpecies

Molecule to parametrize

Returns

GromacsSingleMoleculeParameterSet

Parameter set with paths to ITP and forcefield files

funcparametrize_smirnoff_gromacs(species, smirnoff_config=None) → GromacsSingleMoleculeParameterSet

Parametrize a molecule using OpenFF SMIRNOFF force field.

Uses OpenFF Interchange to generate GROMACS ITP files.

paramspeciesSingleMoleculeSpecies

The molecule species to parametrize.

paramsmirnoff_configSmirnoffConfig

= None

Configuration for SMIRNOFF parametrization. If None, uses defaults.

Returns

GromacsSingleMoleculeParameterSet

The parameter set containing paths to generated ITP files.

funcgenerate_gromacs_topology(u, species, parameters, system_name) → str

Write a GROMACS topology file from species and their parameters.

paramumda.Universe

Universe with the system structure

paramspecieslist

List of species objects

paramparameterslist[GromacsSingleMoleculeParameterSet]

Matching parameter sets for each species

paramsystem_namestr

Name for the [ system ] section

Returns

str