OpenMM
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A ForceField constructs OpenMM System objects based on a Topology. More...
Public Member Functions | |
def | __init__ |
Load one or more XML files and create a ForceField object based on them. More... | |
def | createSystem |
Construct an OpenMM System representing a Topology with this force field. More... | |
A ForceField constructs OpenMM System objects based on a Topology.
def __init__ | ( | self, | |
files | |||
) |
Load one or more XML files and create a ForceField object based on them.
files | A list of XML files defining the force field. Each entry may be an absolute file path, a path relative to the current working directory, or a path relative to this module's data subdirectory (for built in force fields). |
References ForceField._atomClasses, ForceField._atomTypes, ForceField._findAtomTypes(), ForceField._forces, ForceField._scripts, ForceField._templates, ForceField._templateSignatures, GromacsTopFile._MoleculeType.angles, ForceField._SystemData.angles, ForceField._BondData.atom1, ForceField._BondData.atom2, ForceField._SystemData.atomBonds, GromacsTopFile._MoleculeType.atoms, Topology.atoms(), Chain.atoms(), ForceField._SystemData.atoms, Residue.atoms(), ForceField._TemplateData.atoms, ForceField._VirtualSiteData.atoms, ForceField._SystemData.atomType, ForceField._TemplateAtomData.bondedTo, GromacsTopFile._MoleculeType.bonds, Topology.bonds(), ForceField._SystemData.bonds, ForceField._TemplateData.bonds, ForceField.createSystem(), Atom.element, ForceField._TemplateAtomData.element, ForceField._TemplateData.externalBonds, ForceField._TemplateAtomData.externalBonds, ForceField._SystemData.impropers, Chain.index, Residue.index, Atom.index, ForceField._VirtualSiteData.index, ForceField._SystemData.isAngleConstrained, ForceField._BondData.isConstrained, ForceField._BondData.length, HarmonicBondGenerator.length, AmoebaBondGenerator.length, AmoebaUreyBradleyGenerator.length, Element.name, Residue.name, ForceField._TemplateData.name, Atom.name, ForceField._TemplateAtomData.name, Modeller._ResidueData.name, Modeller._Hydrogen.name, ForceField._SystemData.propers, ForceField._TemplateAtomData.type, ForceField._VirtualSiteData.type, AmoebaOutOfPlaneBendGenerator.type, AmoebaVdwGenerator.type, ForceField._SystemData.virtualSites, ForceField._TemplateData.virtualSites, and ForceField._VirtualSiteData.weights.
Referenced by ForceField.createSystem().
def createSystem | ( | self, | |
topology, | |||
nonbondedMethod = NoCutoff , |
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nonbondedCutoff = 1.0*unit.nanometer , |
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constraints = None , |
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rigidWater = True , |
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removeCMMotion = True , |
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hydrogenMass = None , |
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args | |||
) |
Construct an OpenMM System representing a Topology with this force field.
topology | (Topology) The Topology for which to create a System |
nonbondedMethod | (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME. |
nonbondedCutoff | (distance=1*nanometer) The cutoff distance to use for nonbonded interactions |
constraints | (object=None) Specifies which bonds and angles should be implemented with constraints. Allowed values are None, HBonds, AllBonds, or HAngles. |
rigidWater | (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument |
removeCMMotion | (boolean=True) If true, a CMMotionRemover will be added to the System |
hydrogenMass | (mass=None) The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same. |
args | Arbitrary additional keyword arguments may also be specified. This allows extra parameters to be specified that are specific to particular force fields. |
References ForceField.__init__(), ForceField._atomTypes, ForceField._forces, ForceField._scripts, ForceField._templateSignatures, HarmonicAngleGenerator.angle, AmoebaAngleGenerator.angle, RBTorsion.c, CustomGBGenerator.computedValues, NonbondedGenerator.coulomb14scale, CustomGBGenerator.energyTerms, GBVIGenerator.ff, GBVIGenerator.fixedParameters, CustomGBGenerator.functions, CustomBondGenerator.globalParams, CustomAngleGenerator.globalParams, CustomTorsionGenerator.globalParams, CustomGBGenerator.globalParams, PeriodicTorsionGenerator.improper, RBTorsionGenerator.improper, CustomTorsionGenerator.improper, HarmonicBondGenerator.k, HarmonicAngleGenerator.k, PeriodicTorsion.k, AmoebaBondGenerator.k, AmoebaAngleGenerator.k, AmoebaPiTorsionGenerator.k, AmoebaUreyBradleyGenerator.k, ForceField._BondData.length, HarmonicBondGenerator.length, AmoebaBondGenerator.length, AmoebaUreyBradleyGenerator.length, NonbondedGenerator.lj14scale, CMAPTorsion.map, CMAPTorsionGenerator.maps, CustomBondGenerator.paramValues, CustomAngleGenerator.paramValues, CustomTorsion.paramValues, CustomGBGenerator.paramValues, CustomAngleGenerator.perAngleParams, CustomBondGenerator.perBondParams, PeriodicTorsion.periodicity, CustomGBGenerator.perParticleParams, CustomTorsionGenerator.perTorsionParams, PeriodicTorsion.phase, PeriodicTorsionGenerator.proper, RBTorsionGenerator.proper, CustomTorsionGenerator.proper, CMAPTorsionGenerator.torsions, NonbondedGenerator.typeMap, GBSAOBCGenerator.typeMap, GBVIGenerator.typeMap, CustomGBGenerator.typeMap, AmoebaVdwGenerator.typeMap, AmoebaMultipoleGenerator.typeMap, AmoebaWcaDispersionGenerator.typeMap, DrudeGenerator.typeMap, HarmonicBondGenerator.types1, HarmonicAngleGenerator.types1, PeriodicTorsion.types1, RBTorsion.types1, CMAPTorsion.types1, CustomBondGenerator.types1, CustomAngleGenerator.types1, CustomTorsion.types1, AmoebaBondGenerator.types1, AmoebaAngleGenerator.types1, AmoebaOutOfPlaneBendGenerator.types1, AmoebaTorsionGenerator.types1, AmoebaPiTorsionGenerator.types1, AmoebaTorsionTorsionGenerator.types1, AmoebaStretchBendGenerator.types1, AmoebaUreyBradleyGenerator.types1, HarmonicBondGenerator.types2, HarmonicAngleGenerator.types2, PeriodicTorsion.types2, RBTorsion.types2, CMAPTorsion.types2, CustomBondGenerator.types2, CustomAngleGenerator.types2, CustomTorsion.types2, AmoebaBondGenerator.types2, AmoebaAngleGenerator.types2, AmoebaOutOfPlaneBendGenerator.types2, AmoebaTorsionGenerator.types2, AmoebaPiTorsionGenerator.types2, AmoebaTorsionTorsionGenerator.types2, AmoebaStretchBendGenerator.types2, AmoebaUreyBradleyGenerator.types2, HarmonicAngleGenerator.types3, PeriodicTorsion.types3, RBTorsion.types3, CMAPTorsion.types3, CustomAngleGenerator.types3, CustomTorsion.types3, AmoebaAngleGenerator.types3, AmoebaOutOfPlaneBendGenerator.types3, AmoebaTorsionGenerator.types3, AmoebaTorsionTorsionGenerator.types3, AmoebaStretchBendGenerator.types3, AmoebaUreyBradleyGenerator.types3, PeriodicTorsion.types4, RBTorsion.types4, CMAPTorsion.types4, CustomTorsion.types4, AmoebaOutOfPlaneBendGenerator.types4, AmoebaTorsionGenerator.types4, AmoebaTorsionTorsionGenerator.types4, CMAPTorsion.types5, and AmoebaTorsionTorsionGenerator.types5.
Referenced by ForceField.__init__().