Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
|
Z
_
__abs__() (openmm.unit.quantity.Quantity method)
__add__() (openmm.unit.quantity.Quantity method)
(openmm.vec3.Vec3 method)
__copy__() (openmm.openmm.State method)
(openmm.openmm.System method)
(openmm.unit.quantity.Quantity method)
__deepcopy__() (openmm.unit.quantity.Quantity method)
__div__() (openmm.unit.quantity.Quantity method)
(openmm.unit.unit.Unit method)
(openmm.vec3.Vec3 method)
__eq__() (openmm.openmm.Continuous1DFunction method)
(openmm.openmm.Continuous2DFunction method)
(openmm.openmm.Continuous3DFunction method)
(openmm.openmm.Discrete1DFunction method)
(openmm.openmm.Discrete2DFunction method)
(openmm.openmm.Discrete3DFunction method)
(openmm.openmm.TabulatedFunction method)
(openmm.unit.quantity.Quantity method)
__getattr__() (openmm.unit.quantity.Quantity method)
__getitem__() (openmm.unit.quantity.Quantity method)
__getnewargs__() (openmm.vec3.Vec3 method)
__hash__() (openmm.unit.basedimension.BaseDimension method)
(openmm.unit.unit.Unit method)
__init__() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.app.amberinpcrdfile.AmberInpcrdFile method)
(openmm.app.amberprmtopfile.AmberPrmtopFile method)
(openmm.app.charmmcrdfiles.CharmmCrdFile method)
(openmm.app.charmmcrdfiles.CharmmRstFile method)
(openmm.app.charmmparameterset.CharmmParameterSet method)
(openmm.app.charmmpsffile.CharmmPsfFile method)
(openmm.app.checkpointreporter.CheckpointReporter method)
(openmm.app.dcdfile.DCDFile method)
(openmm.app.dcdreporter.DCDReporter method)
(openmm.app.desmonddmsfile.DesmondDMSFile method)
(openmm.app.element.Element method)
(openmm.app.forcefield.ForceField method)
(openmm.app.gromacsgrofile.GromacsGroFile method)
(openmm.app.gromacstopfile.GromacsTopFile method)
(openmm.app.internal.charmm.exceptions.CharmmPSFWarning method)
(openmm.app.metadynamics.BiasVariable method)
(openmm.app.metadynamics.Metadynamics method)
(openmm.app.modeller.Modeller method)
(openmm.app.pdbfile.PDBFile method)
(openmm.app.pdbreporter.PDBReporter method)
(openmm.app.pdbreporter.PDBxReporter method)
(openmm.app.pdbxfile.PDBxFile method)
(openmm.app.simulatedtempering.SimulatedTempering method)
(openmm.app.simulation.Simulation method)
(openmm.app.statedatareporter.StateDataReporter method)
(openmm.app.topology.Atom method)
(openmm.app.topology.Chain method)
(openmm.app.topology.Residue method)
(openmm.app.topology.Topology method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaTorsionTorsionForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.AndersenThermostat method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CMMotionRemover method)
(openmm.openmm.CompoundIntegrator method)
(openmm.openmm.Context method)
(openmm.openmm.Continuous1DFunction method)
(openmm.openmm.Continuous2DFunction method)
(openmm.openmm.Continuous3DFunction method)
(openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.Discrete1DFunction method)
(openmm.openmm.Discrete2DFunction method)
(openmm.openmm.Discrete3DFunction method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.Force method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HarmonicAngleForce method)
(openmm.openmm.HarmonicBondForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.Integrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.LocalCoordinatesSite method)
(openmm.openmm.LocalEnergyMinimizer method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.NonbondedForce method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.OutOfPlaneSite method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.Platform method)
(openmm.openmm.RBTorsionForce method)
(openmm.openmm.RMSDForce method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.RPMDMonteCarloBarostat method)
(openmm.openmm.SerializationNode method)
(openmm.openmm.SerializationProxy method)
(openmm.openmm.State method)
(openmm.openmm.System method)
(openmm.openmm.TabulatedFunction method)
(openmm.openmm.ThreeParticleAverageSite method)
(openmm.openmm.TwoParticleAverageSite method)
(openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
(openmm.openmm.VerletIntegrator method)
(openmm.openmm.VirtualSite method)
(openmm.openmm.XmlSerializer method)
(openmm.OpenMMException method)
(openmm.unit.basedimension.BaseDimension method)
(openmm.unit.baseunit.BaseUnit method)
(openmm.unit.prefix.SiPrefix method)
(openmm.unit.quantity.Quantity method)
(openmm.unit.unit.ScaledUnit method)
(openmm.unit.unit.Unit method)
(openmm.unit.unit.UnitSystem method)
(openmm.vec3.Vec3 method)
__len__() (openmm.unit.quantity.Quantity method)
__lt__() (openmm.unit.basedimension.BaseDimension method)
(openmm.unit.baseunit.BaseUnit method)
(openmm.unit.unit.ScaledUnit method)
(openmm.unit.unit.Unit method)
__mul__() (openmm.unit.prefix.SiPrefix method)
(openmm.unit.quantity.Quantity method)
(openmm.vec3.Vec3 method)
__ne__() (openmm.openmm.Continuous1DFunction method)
(openmm.openmm.Continuous2DFunction method)
(openmm.openmm.Continuous3DFunction method)
(openmm.openmm.Discrete1DFunction method)
(openmm.openmm.Discrete2DFunction method)
(openmm.openmm.Discrete3DFunction method)
(openmm.openmm.TabulatedFunction method)
(openmm.unit.quantity.Quantity method)
__neg__() (openmm.unit.quantity.Quantity method)
__new__() (openmm.vec3.Vec3 static method)
__nonzero__() (openmm.unit.quantity.Quantity method)
__pos__() (openmm.unit.quantity.Quantity method)
__pow__() (openmm.unit.quantity.Quantity method)
(openmm.unit.unit.Unit method)
__radd__() (openmm.vec3.Vec3 method)
__rdiv__() (openmm.unit.quantity.Quantity method)
__repr__() (openmm.unit.quantity.Quantity method)
(openmm.unit.unit.ScaledUnit method)
(openmm.unit.unit.Unit method)
__rmul__() (openmm.unit.quantity.Quantity method)
(openmm.vec3.Vec3 method)
__rsub__() (openmm.vec3.Vec3 method)
__rtruediv__() (openmm.unit.quantity.Quantity method)
__str__() (openmm.unit.baseunit.BaseUnit method)
(openmm.unit.quantity.Quantity method)
(openmm.unit.unit.ScaledUnit method)
(openmm.unit.unit.Unit method)
(openmm.unit.unit.UnitSystem method)
__sub__() (openmm.unit.quantity.Quantity method)
(openmm.vec3.Vec3 method)
__truediv__() (openmm.unit.quantity.Quantity method)
(openmm.unit.unit.Unit method)
(openmm.vec3.Vec3 method)
A
add() (openmm.app.modeller.Modeller method)
addAcceptor() (openmm.openmm.CustomHbondForce method)
addAngle() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.HarmonicAngleForce method)
addAtom() (openmm.app.topology.Topology method)
addBond() (openmm.app.topology.Topology method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.HarmonicBondForce method)
addChain() (openmm.app.topology.Topology method)
addCollectiveVariable() (openmm.openmm.CustomCVForce method)
addComputedValue() (openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomNonbondedForce method)
addComputeGlobal() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
addComputePerDof() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
addComputeSum() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
addConstrainPositions() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
addConstraint() (openmm.openmm.System method)
addConstrainVelocities() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
addDonor() (openmm.openmm.CustomHbondForce method)
addEnergyParameterDerivative() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
addEnergyTerm() (openmm.openmm.CustomGBForce method)
addException() (openmm.openmm.GayBerneForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
addException_usingRMin() (openmm.openmm.NonbondedForce method)
addExceptionParameterOffset() (openmm.openmm.NonbondedForce method)
addExclusion() (openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
addExtraParticles() (openmm.app.modeller.Modeller method)
addForce() (openmm.openmm.System method)
addFunction() (openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomNonbondedForce method)
addGlobalParameter() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.NonbondedForce method)
addGlobalVariable() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
addGroup() (openmm.openmm.CustomCentroidBondForce method)
addHydrogens() (openmm.app.modeller.Modeller method)
addIntegrator() (openmm.openmm.CompoundIntegrator method)
addInteractionGroup() (openmm.openmm.CustomNonbondedForce method)
addMap() (openmm.openmm.CMAPTorsionForce method)
addMembrane() (openmm.app.modeller.Modeller method)
addMultipole() (openmm.openmm.AmoebaMultipoleForce method)
addParticle() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
(openmm.openmm.System method)
addParticle_usingRVdw() (openmm.openmm.NonbondedForce method)
addParticleParameterOffset() (openmm.openmm.NonbondedForce method)
addParticleType() (openmm.openmm.AmoebaVdwForce method)
addPerAcceptorParameter() (openmm.openmm.CustomHbondForce method)
addPerAngleParameter() (openmm.openmm.CustomAngleForce method)
addPerBondParameter() (openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
addPerDofVariable() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
addPerDonorParameter() (openmm.openmm.CustomHbondForce method)
addPerParticleParameter() (openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
addPerTorsionParameter() (openmm.openmm.CustomTorsionForce method)
addResidue() (openmm.app.topology.Topology method)
addScreenedPair() (openmm.openmm.DrudeForce method)
addSolvent() (openmm.app.modeller.Modeller method)
addSubsystemThermostat() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
addTabulatedFunction() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
addThermostat() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
addTorsion() (openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
addTorsionTorsion() (openmm.openmm.AmoebaTorsionTorsionForce method)
addTypePair() (openmm.openmm.AmoebaVdwForce method)
addUpdateContextState() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
AmberInpcrdFile (class in openmm.app.amberinpcrdfile)
AmberPrmtopFile (class in openmm.app.amberprmtopfile)
AMDForceGroupIntegrator (class in openmm.amd)
AMDIntegrator (class in openmm.amd)
AmoebaGeneralizedKirkwoodForce (class in openmm.openmm)
AmoebaMultipoleForce (class in openmm.openmm)
AmoebaTorsionTorsionForce (class in openmm.openmm)
AmoebaVdwForce (class in openmm.openmm)
AmoebaWcaDispersionForce (class in openmm.openmm)
AndersenThermostat (class in openmm.openmm)
applyConstraints() (openmm.openmm.Context method)
applyVelocityConstraints() (openmm.openmm.Context method)
Atom (class in openmm.app.topology)
atoms() (openmm.app.topology.Chain method)
(openmm.app.topology.Residue method)
(openmm.app.topology.Topology method)
B
BaseDimension (class in openmm.unit.basedimension)
BaseUnit (class in openmm.unit.baseunit)
beginIfBlock() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
beginWhileBlock() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
BiasVariable (class in openmm.app.metadynamics)
bonds() (openmm.app.topology.Residue method)
(openmm.app.topology.Topology method)
boxLengths (openmm.app.charmmpsffile.CharmmPsfFile property)
boxVectors (openmm.app.charmmpsffile.CharmmPsfFile property)
BrownianIntegrator (class in openmm.openmm)
C
Chain (class in openmm.app.topology)
chains() (openmm.app.topology.Topology method)
CharmmCrdFile (class in openmm.app.charmmcrdfiles)
CharmmParameterSet (class in openmm.app.charmmparameterset)
CharmmPsfFile (class in openmm.app.charmmpsffile)
CharmmPSFWarning (class in openmm.app.internal.charmm.exceptions)
CharmmRstFile (class in openmm.app.charmmcrdfiles)
CheckpointReporter (class in openmm.app.checkpointreporter)
clone() (openmm.openmm.XmlSerializer static method)
close() (openmm.app.desmonddmsfile.DesmondDMSFile method)
CMAPTorsionForce (class in openmm.openmm)
CMMotionRemover (class in openmm.openmm)
CollisionFrequency() (openmm.openmm.AndersenThermostat static method)
CompoundIntegrator (class in openmm.openmm)
computeDrudeKineticEnergy() (openmm.openmm.DrudeNoseHooverIntegrator method)
computeDrudeTemperature() (openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
computeHeatBathEnergy() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
computeSystemTemperature() (openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
computeTotalKineticEnergy() (openmm.openmm.DrudeNoseHooverIntegrator method)
computeVirtualSites() (openmm.openmm.Context method)
condense() (openmm.app.charmmparameterset.CharmmParameterSet method)
Context (class in openmm.openmm)
Continuous1DFunction (class in openmm.openmm)
Continuous2DFunction (class in openmm.openmm)
Continuous3DFunction (class in openmm.openmm)
conversion_factor_to() (openmm.unit.baseunit.BaseUnit method)
(openmm.unit.unit.Unit method)
convertWater() (openmm.app.modeller.Modeller method)
Copy() (openmm.openmm.Continuous1DFunction method)
(openmm.openmm.Continuous2DFunction method)
(openmm.openmm.Continuous3DFunction method)
(openmm.openmm.Discrete1DFunction method)
(openmm.openmm.Discrete2DFunction method)
(openmm.openmm.Discrete3DFunction method)
(openmm.openmm.TabulatedFunction method)
count() (openmm.vec3.Vec3 method)
create_unit() (openmm.unit.unit.Unit method)
createCheckpoint() (openmm.openmm.Context method)
createChildNode() (openmm.openmm.SerializationNode method)
createDisulfideBonds() (openmm.app.topology.Topology method)
createExceptionsFromBonds() (openmm.openmm.NonbondedForce method)
createExclusionsFromBonds() (openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
createStandardBonds() (openmm.app.topology.Topology method)
createSystem() (openmm.app.amberprmtopfile.AmberPrmtopFile method)
(openmm.app.charmmpsffile.CharmmPsfFile method)
(openmm.app.desmonddmsfile.DesmondDMSFile method)
(openmm.app.forcefield.ForceField method)
(openmm.app.gromacstopfile.GromacsTopFile method)
currentStep (openmm.app.simulation.Simulation property)
CustomAngleForce (class in openmm.openmm)
CustomBondForce (class in openmm.openmm)
CustomCentroidBondForce (class in openmm.openmm)
CustomCompoundBondForce (class in openmm.openmm)
CustomCVForce (class in openmm.openmm)
CustomExternalForce (class in openmm.openmm)
CustomGBForce (class in openmm.openmm)
CustomHbondForce (class in openmm.openmm)
CustomIntegrator (class in openmm.openmm)
CustomManyParticleForce (class in openmm.openmm)
CustomNonbondedForce (class in openmm.openmm)
CustomTorsionForce (class in openmm.openmm)
D
DCDFile (class in openmm.app.dcdfile)
DCDReporter (class in openmm.app.dcdreporter)
define_conversion_factor_to() (openmm.unit.baseunit.BaseUnit method)
delete() (openmm.app.modeller.Modeller method)
deleteCmap() (openmm.app.charmmpsffile.CharmmPsfFile method)
deleteWater() (openmm.app.modeller.Modeller method)
describeNextReport() (openmm.app.checkpointreporter.CheckpointReporter method)
(openmm.app.dcdreporter.DCDReporter method)
(openmm.app.pdbreporter.PDBReporter method)
(openmm.app.pdbreporter.PDBxReporter method)
(openmm.app.statedatareporter.StateDataReporter method)
deserialize() (openmm.openmm.SerializationProxy method)
(openmm.openmm.XmlSerializer static method)
deserializeSystem() (openmm.openmm.XmlSerializer static method)
DesmondDMSFile (class in openmm.app.desmonddmsfile)
Discrete1DFunction (class in openmm.openmm)
Discrete2DFunction (class in openmm.openmm)
Discrete3DFunction (class in openmm.openmm)
DrudeForce (class in openmm.openmm)
DrudeIntegrator (class in openmm.openmm)
DrudeLangevinIntegrator (class in openmm.openmm)
DrudeNoseHooverIntegrator (class in openmm.openmm)
DrudeSCFIntegrator (class in openmm.openmm)
DualAMDIntegrator (class in openmm.amd)
E
Element (class in openmm.app.element)
endBlock() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
express_unit() (openmm.unit.unit.UnitSystem method)
external_bonds() (openmm.app.topology.Residue method)
F
findPlatform() (openmm.openmm.Platform static method)
Force (class in openmm.openmm)
ForceField (class in openmm.app.forcefield)
G
GayBerneForce (class in openmm.openmm)
GBSAOBCForce (class in openmm.openmm)
generateTemplatesForUnmatchedResidues() (openmm.app.forcefield.ForceField method)
get_conversion_factor_to_base_units() (openmm.unit.unit.Unit method)
get_dimension_tuple() (openmm.unit.baseunit.BaseUnit method)
(openmm.unit.unit.ScaledUnit method)
get_name() (openmm.unit.unit.Unit method)
get_symbol() (openmm.unit.unit.Unit method)
getAcceptorParameters() (openmm.openmm.CustomHbondForce method)
getAEwald() (openmm.openmm.AmoebaMultipoleForce method)
getAlchemicalMethod() (openmm.openmm.AmoebaVdwForce method)
getAlpha() (openmm.amd.AMDIntegrator method)
getAlphaGroup() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.DualAMDIntegrator method)
getAlphaTotal() (openmm.amd.DualAMDIntegrator method)
getAngleParameters() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.HarmonicAngleForce method)
getApplyThermostat() (openmm.openmm.RPMDIntegrator method)
getAwater() (openmm.openmm.AmoebaWcaDispersionForce method)
getBondParameters() (openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.HarmonicBondForce method)
getBoolProperty() (openmm.openmm.SerializationNode method)
getBoxVectors() (openmm.app.amberinpcrdfile.AmberInpcrdFile method)
getByMass() (openmm.app.element.Element static method)
getBySymbol() (openmm.app.element.Element static method)
getChainID() (openmm.openmm.NoseHooverChain method)
getChainLength() (openmm.openmm.NoseHooverChain method)
getChildNode() (openmm.openmm.SerializationNode method)
getChildren() (openmm.openmm.SerializationNode method)
getCollectiveVariable() (openmm.openmm.CustomCVForce method)
getCollectiveVariableName() (openmm.openmm.CustomCVForce method)
getCollectiveVariables() (openmm.app.metadynamics.Metadynamics method)
getCollectiveVariableValues() (openmm.openmm.CustomCVForce method)
getCollisionFrequency() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.NoseHooverIntegrator method)
getComputationStep() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getComputedValueParameters() (openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomNonbondedForce method)
getConstraintParameters() (openmm.openmm.System method)
getConstraintTolerance() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CompoundIntegrator method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.Integrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
(openmm.openmm.VerletIntegrator method)
getContractions() (openmm.openmm.RPMDIntegrator method)
getCovalentMap() (openmm.openmm.AmoebaMultipoleForce method)
getCovalentMaps() (openmm.openmm.AmoebaMultipoleForce method)
getCurrentIntegrator() (openmm.openmm.CompoundIntegrator method)
getCutoff() (openmm.openmm.AmoebaVdwForce method)
getCutoffDistance() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
getDataTypes() (openmm.openmm.State method)
getDefaultCollisionFrequency() (openmm.openmm.AndersenThermostat method)
getDefaultPeriodicBoxVectors() (openmm.openmm.System method)
getDefaultPluginsDirectory() (openmm.openmm.Platform static method)
getDefaultPressure() (openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.RPMDMonteCarloBarostat method)
getDefaultSurfaceTension() (openmm.openmm.MonteCarloMembraneBarostat method)
getDefaultTemperature() (openmm.openmm.AndersenThermostat method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
getDispoff() (openmm.openmm.AmoebaWcaDispersionForce method)
getDonorParameters() (openmm.openmm.CustomHbondForce method)
getDoubleProperty() (openmm.openmm.SerializationNode method)
getDPMEParameters() (openmm.openmm.HippoNonbondedForce method)
getDPMEParametersInContext() (openmm.openmm.HippoNonbondedForce method)
getDrudeFriction() (openmm.openmm.DrudeLangevinIntegrator method)
getDrudeTemperature() (openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
getE() (openmm.amd.AMDIntegrator method)
getEffectiveEnergy() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
getEGroup() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.DualAMDIntegrator method)
getElectrostaticPotential() (openmm.openmm.AmoebaMultipoleForce method)
getEnergyFunction() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
getEnergyParameterDerivativeName() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
getEnergyParameterDerivatives() (openmm.openmm.State method)
getEnergyTermParameters() (openmm.openmm.CustomGBForce method)
getEpsh() (openmm.openmm.AmoebaWcaDispersionForce method)
getEpsilonCombiningRule() (openmm.openmm.AmoebaVdwForce method)
getEpso() (openmm.openmm.AmoebaWcaDispersionForce method)
getErrorTolerance() (openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
getETotal() (openmm.amd.DualAMDIntegrator method)
getEwaldErrorTolerance() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
getExceptionParameterOffset() (openmm.openmm.NonbondedForce method)
getExceptionParameters() (openmm.openmm.GayBerneForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
getExceptionsUsePeriodicBoundaryConditions() (openmm.openmm.NonbondedForce method)
getExclusionParticles() (openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
getExtrapolationCoefficients() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.HippoNonbondedForce method)
getForce() (openmm.openmm.System method)
getForceGroup() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaTorsionTorsionForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.AndersenThermostat method)
(openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CMMotionRemover method)
(openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.Force method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HarmonicAngleForce method)
(openmm.openmm.HarmonicBondForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.NonbondedForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
(openmm.openmm.RMSDForce method)
(openmm.openmm.RPMDMonteCarloBarostat method)
getForces() (openmm.openmm.State method)
(openmm.openmm.System method)
getFreeEnergy() (openmm.app.metadynamics.Metadynamics method)
getFrequency() (openmm.openmm.CMMotionRemover method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.RPMDMonteCarloBarostat method)
getFriction() (openmm.openmm.BrownianIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
getFunctionParameters() (openmm.openmm.Continuous1DFunction method)
(openmm.openmm.Continuous2DFunction method)
(openmm.openmm.Continuous3DFunction method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.Discrete1DFunction method)
(openmm.openmm.Discrete2DFunction method)
(openmm.openmm.Discrete3DFunction method)
getGenerators() (openmm.app.forcefield.ForceField method)
getGlobalParameterDefaultValue() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.NonbondedForce method)
getGlobalParameterName() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.NonbondedForce method)
getGlobalVariable() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getGlobalVariableByName() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getGlobalVariableName() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getGroupParameters() (openmm.openmm.CustomCentroidBondForce method)
getIncludeCavityTerm() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
getIncludeDirectSpace() (openmm.openmm.NonbondedForce method)
getInducedDipoles() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.HippoNonbondedForce method)
getInnerContext() (openmm.openmm.CustomCVForce method)
getIntegrationForceGroups() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CompoundIntegrator method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.Integrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
(openmm.openmm.VerletIntegrator method)
getIntegrator() (openmm.openmm.CompoundIntegrator method)
getInteractionGroupParameters() (openmm.openmm.CustomNonbondedForce method)
getIntProperty() (openmm.openmm.SerializationNode method)
getKineticEnergy() (openmm.openmm.State method)
getKineticEnergyExpression() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getLabFramePermanentDipoles() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.HippoNonbondedForce method)
getLJPMEParameters() (openmm.openmm.NonbondedForce method)
getLJPMEParametersInContext() (openmm.openmm.NonbondedForce method)
getLocalPosition() (openmm.openmm.LocalCoordinatesSite method)
getLongProperty() (openmm.openmm.SerializationNode method)
getMapParameters() (openmm.openmm.CMAPTorsionForce method)
getMatchingTemplates() (openmm.app.forcefield.ForceField method)
getMaxDrudeDistance() (openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
getMaximumPairDistance() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
getMaximumStepSize() (openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
getMinimizationErrorTolerance() (openmm.openmm.DrudeSCFIntegrator method)
getMolecules() (openmm.openmm.Context method)
getMultipoleParameters() (openmm.openmm.AmoebaMultipoleForce method)
getMutualInducedMaxIterations() (openmm.openmm.AmoebaMultipoleForce method)
getMutualInducedTargetEpsilon() (openmm.openmm.AmoebaMultipoleForce method)
getName() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaTorsionTorsionForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.AndersenThermostat method)
(openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CMMotionRemover method)
(openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.Force method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HarmonicAngleForce method)
(openmm.openmm.HarmonicBondForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.NonbondedForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.Platform method)
(openmm.openmm.RBTorsionForce method)
(openmm.openmm.RMSDForce method)
(openmm.openmm.RPMDMonteCarloBarostat method)
(openmm.openmm.SerializationNode method)
getNonbondedMethod() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
getNumAcceptors() (openmm.openmm.CustomHbondForce method)
getNumAngles() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.HarmonicAngleForce method)
getNumAtoms() (openmm.app.topology.Topology method)
getNumBonds() (openmm.app.topology.Topology method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.HarmonicBondForce method)
getNumChains() (openmm.app.topology.Topology method)
getNumCollectiveVariables() (openmm.openmm.CustomCVForce method)
getNumComputations() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getNumComputedValues() (openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomNonbondedForce method)
getNumConstraints() (openmm.openmm.System method)
getNumCopies() (openmm.openmm.RPMDIntegrator method)
getNumDegreesOfFreedom() (openmm.openmm.NoseHooverChain method)
getNumDonors() (openmm.openmm.CustomHbondForce method)
getNumEnergyParameterDerivatives() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
getNumEnergyTerms() (openmm.openmm.CustomGBForce method)
getNumExceptionParameterOffsets() (openmm.openmm.NonbondedForce method)
getNumExceptions() (openmm.openmm.GayBerneForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
getNumExclusions() (openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
getNumForces() (openmm.openmm.System method)
getNumFrames() (openmm.app.gromacsgrofile.GromacsGroFile method)
(openmm.app.pdbfile.PDBFile method)
(openmm.app.pdbxfile.PDBxFile method)
getNumFunctions() (openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomNonbondedForce method)
getNumGlobalParameters() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.NonbondedForce method)
getNumGlobalVariables() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getNumGroups() (openmm.openmm.CustomCentroidBondForce method)
getNumGroupsPerBond() (openmm.openmm.CustomCentroidBondForce method)
getNumIntegrators() (openmm.openmm.CompoundIntegrator method)
getNumInteractionGroups() (openmm.openmm.CustomNonbondedForce method)
getNumMaps() (openmm.openmm.CMAPTorsionForce method)
getNumMultipoles() (openmm.openmm.AmoebaMultipoleForce method)
getNumMultiTimeSteps() (openmm.openmm.NoseHooverChain method)
getNumParticleParameterOffsets() (openmm.openmm.NonbondedForce method)
getNumParticles() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.LocalCoordinatesSite method)
(openmm.openmm.NonbondedForce method)
(openmm.openmm.OutOfPlaneSite method)
(openmm.openmm.System method)
(openmm.openmm.ThreeParticleAverageSite method)
(openmm.openmm.TwoParticleAverageSite method)
(openmm.openmm.VirtualSite method)
getNumParticlesPerBond() (openmm.openmm.CustomCompoundBondForce method)
getNumParticlesPerSet() (openmm.openmm.CustomManyParticleForce method)
getNumParticleTypes() (openmm.openmm.AmoebaVdwForce method)
getNumPerAcceptorParameters() (openmm.openmm.CustomHbondForce method)
getNumPerAngleParameters() (openmm.openmm.CustomAngleForce method)
getNumPerBondParameters() (openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
getNumPerDofVariables() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getNumPerDonorParameters() (openmm.openmm.CustomHbondForce method)
getNumPerParticleParameters() (openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
getNumPerTorsionParameters() (openmm.openmm.CustomTorsionForce method)
getNumPlatforms() (openmm.openmm.Platform static method)
getNumResidues() (openmm.app.topology.Topology method)
getNumScreenedPairs() (openmm.openmm.DrudeForce method)
getNumTabulatedFunctions() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
getNumThermostats() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
getNumTorsions() (openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
getNumTorsionTorsionGrids() (openmm.openmm.AmoebaTorsionTorsionForce method)
getNumTorsionTorsions() (openmm.openmm.AmoebaTorsionTorsionForce method)
getNumTypePairs() (openmm.openmm.AmoebaVdwForce method)
getNumYoshidaSuzukiTimeSteps() (openmm.openmm.NoseHooverChain method)
getOpenMMVersion() (openmm.openmm.Platform static method)
getOriginWeights() (openmm.openmm.LocalCoordinatesSite method)
getParameter() (openmm.openmm.Context method)
getParameters() (openmm.openmm.Context method)
(openmm.openmm.State method)
getParticle() (openmm.openmm.LocalCoordinatesSite method)
(openmm.openmm.OutOfPlaneSite method)
(openmm.openmm.ThreeParticleAverageSite method)
(openmm.openmm.TwoParticleAverageSite method)
(openmm.openmm.VirtualSite method)
getParticleExclusions() (openmm.openmm.AmoebaVdwForce method)
getParticleMass() (openmm.openmm.System method)
getParticleParameterOffset() (openmm.openmm.NonbondedForce method)
getParticleParameters() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
getParticles() (openmm.openmm.RMSDForce method)
getParticleTypeParameters() (openmm.openmm.AmoebaVdwForce method)
getPerAcceptorParameterName() (openmm.openmm.CustomHbondForce method)
getPerAngleParameterName() (openmm.openmm.CustomAngleForce method)
getPerBondParameterName() (openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
getPerDofVariable() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getPerDofVariableByName() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getPerDofVariableName() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
getPerDonorParameterName() (openmm.openmm.CustomHbondForce method)
getPeriodic() (openmm.openmm.Continuous1DFunction method)
(openmm.openmm.Continuous2DFunction method)
(openmm.openmm.Continuous3DFunction method)
(openmm.openmm.Discrete1DFunction method)
(openmm.openmm.Discrete2DFunction method)
(openmm.openmm.Discrete3DFunction method)
(openmm.openmm.TabulatedFunction method)
getPeriodicBoxVectors() (openmm.app.gromacsgrofile.GromacsGroFile method)
(openmm.app.topology.Topology method)
(openmm.openmm.State method)
getPeriodicBoxVolume() (openmm.openmm.State method)
getPermutationMode() (openmm.openmm.CustomManyParticleForce method)
getPerParticleParameterName() (openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
getPerTorsionParameterName() (openmm.openmm.CustomTorsionForce method)
getPlatform() (openmm.openmm.Context method)
(openmm.openmm.Platform static method)
getPlatformByName() (openmm.openmm.Platform static method)
getPluginLoadFailures() (openmm.openmm.Platform static method)
getPmeBSplineOrder() (openmm.openmm.AmoebaMultipoleForce method)
getPmeGridDimensions() (openmm.openmm.AmoebaMultipoleForce method)
getPMEParameters() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
getPMEParametersInContext() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
getPolarizationType() (openmm.openmm.AmoebaMultipoleForce method)
getPositions() (openmm.app.amberinpcrdfile.AmberInpcrdFile method)
(openmm.app.desmonddmsfile.DesmondDMSFile method)
(openmm.app.gromacsgrofile.GromacsGroFile method)
(openmm.app.modeller.Modeller method)
(openmm.app.pdbfile.PDBFile method)
(openmm.app.pdbxfile.PDBxFile method)
(openmm.openmm.State method)
getPotentialEnergy() (openmm.openmm.State method)
getPotentialFunction() (openmm.openmm.AmoebaVdwForce method)
getProbeRadius() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
getProperties() (openmm.openmm.SerializationNode method)
getPropertyDefaultValue() (openmm.openmm.Platform method)
getPropertyNames() (openmm.openmm.Platform method)
getPropertyValue() (openmm.openmm.Platform method)
getProvenance() (openmm.app.desmonddmsfile.DesmondDMSFile method)
getProxy() (openmm.openmm.SerializationProxy static method)
getRandomNumberSeed() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.AndersenThermostat method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.RPMDMonteCarloBarostat method)
(openmm.openmm.VariableLangevinIntegrator method)
getReactionFieldDielectric() (openmm.openmm.NonbondedForce method)
getReciprocalSpaceForceGroup() (openmm.openmm.NonbondedForce method)
getReferencePositions() (openmm.openmm.RMSDForce method)
getRelativeCollisionFrequency() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.NoseHooverIntegrator method)
getRelativeTemperature() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.NoseHooverIntegrator method)
getRminh() (openmm.openmm.AmoebaWcaDispersionForce method)
getRmino() (openmm.openmm.AmoebaWcaDispersionForce method)
getScaleMoleculesAsRigid() (openmm.openmm.MonteCarloFlexibleBarostat method)
getScaleX() (openmm.openmm.MonteCarloAnisotropicBarostat method)
getScaleY() (openmm.openmm.MonteCarloAnisotropicBarostat method)
getScaleZ() (openmm.openmm.MonteCarloAnisotropicBarostat method)
getScreenedPairParameters() (openmm.openmm.DrudeForce method)
getShctd() (openmm.openmm.AmoebaWcaDispersionForce method)
getSigmaCombiningRule() (openmm.openmm.AmoebaVdwForce method)
getSlevy() (openmm.openmm.AmoebaWcaDispersionForce method)
getSoftcoreAlpha() (openmm.openmm.AmoebaVdwForce method)
getSoftcorePower() (openmm.openmm.AmoebaVdwForce method)
getSoluteDielectric() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.GBSAOBCForce method)
getSolventDielectric() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.GBSAOBCForce method)
getSpeed() (openmm.openmm.Platform method)
getState() (openmm.openmm.Context method)
(openmm.openmm.RPMDIntegrator method)
getStepCount() (openmm.openmm.Context method)
(openmm.openmm.State method)
getStepSize() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CompoundIntegrator method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.Integrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
(openmm.openmm.VerletIntegrator method)
getStringProperty() (openmm.openmm.SerializationNode method)
getSurfaceAreaEnergy() (openmm.openmm.GBSAOBCForce method)
getSurfaceAreaFactor() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
getSwitchingDistance() (openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
getSystem() (openmm.openmm.Context method)
getSystemMultipoleMoments() (openmm.openmm.AmoebaMultipoleForce method)
getTabulatedFunction() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
getTabulatedFunctionName() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
getTemperature() (openmm.openmm.BrownianIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
getThermostat() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
getThermostatedAtoms() (openmm.openmm.NoseHooverChain method)
getThermostatedPairs() (openmm.openmm.NoseHooverChain method)
getTime() (openmm.openmm.Context method)
(openmm.openmm.State method)
getTopology() (openmm.app.desmonddmsfile.DesmondDMSFile method)
(openmm.app.modeller.Modeller method)
(openmm.app.pdbfile.PDBFile method)
(openmm.app.pdbxfile.PDBxFile method)
getTorsionParameters() (openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
getTorsionTorsionGrid() (openmm.openmm.AmoebaTorsionTorsionForce method)
getTorsionTorsionParameters() (openmm.openmm.AmoebaTorsionTorsionForce method)
getTotalDipoles() (openmm.openmm.AmoebaMultipoleForce method)
getTotalEnergy() (openmm.openmm.RPMDIntegrator method)
getTypeFilter() (openmm.openmm.CustomManyParticleForce method)
getTypeName() (openmm.openmm.SerializationProxy method)
getTypePairParameters() (openmm.openmm.AmoebaVdwForce method)
getUnitCellDimensions() (openmm.app.gromacsgrofile.GromacsGroFile method)
(openmm.app.topology.Topology method)
getUnmatchedResidues() (openmm.app.forcefield.ForceField method)
getUpdateCount() (openmm.openmm.Continuous1DFunction method)
(openmm.openmm.Continuous2DFunction method)
(openmm.openmm.Continuous3DFunction method)
(openmm.openmm.Discrete1DFunction method)
(openmm.openmm.Discrete2DFunction method)
(openmm.openmm.Discrete3DFunction method)
(openmm.openmm.TabulatedFunction method)
getUseDispersionCorrection() (openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.NonbondedForce method)
getUseLongRangeCorrection() (openmm.openmm.CustomNonbondedForce method)
getUseParticleTypes() (openmm.openmm.AmoebaVdwForce method)
getUseSwitchingFunction() (openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.NonbondedForce method)
getVelocities() (openmm.app.amberinpcrdfile.AmberInpcrdFile method)
(openmm.app.desmonddmsfile.DesmondDMSFile method)
(openmm.openmm.State method)
getVirtualSite() (openmm.openmm.System method)
getWeight() (openmm.openmm.ThreeParticleAverageSite method)
(openmm.openmm.TwoParticleAverageSite method)
getWeight12() (openmm.openmm.OutOfPlaneSite method)
getWeight13() (openmm.openmm.OutOfPlaneSite method)
getWeightCross() (openmm.openmm.OutOfPlaneSite method)
getXWeights() (openmm.openmm.LocalCoordinatesSite method)
getXYMode() (openmm.openmm.MonteCarloMembraneBarostat method)
getYoshidaSuzukiWeights() (openmm.openmm.NoseHooverChain method)
getYWeights() (openmm.openmm.LocalCoordinatesSite method)
getZMode() (openmm.openmm.MonteCarloMembraneBarostat method)
GromacsGroFile (class in openmm.app.gromacsgrofile)
GromacsTopFile (class in openmm.app.gromacstopfile)
H
HarmonicAngleForce (class in openmm.openmm)
HarmonicBondForce (class in openmm.openmm)
hasProperty() (openmm.openmm.SerializationNode method)
hasSubsystemThermostats() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
helpful (openmm.app.charmmparameterset.CharmmParameterSet attribute)
HippoNonbondedForce (class in openmm.openmm)
I
in_unit_system() (openmm.unit.quantity.Quantity method)
(openmm.unit.unit.Unit method)
in_units_of() (openmm.unit.quantity.Quantity method)
index() (openmm.vec3.Vec3 method)
initialize() (openmm.openmm.DrudeNoseHooverIntegrator method)
Integrator (class in openmm.openmm)
internal_bonds() (openmm.app.topology.Residue method)
is_compatible() (openmm.unit.unit.Unit method)
is_dimensionless() (openmm.unit.unit.Unit method)
isVirtualSite() (openmm.openmm.System method)
iter_all_base_units() (openmm.unit.unit.Unit method)
iter_base_dimensions() (openmm.unit.baseunit.BaseUnit method)
(openmm.unit.unit.ScaledUnit method)
(openmm.unit.unit.Unit method)
iter_top_base_units() (openmm.unit.unit.Unit method)
L
Lambda() (openmm.openmm.AmoebaVdwForce static method)
LangevinIntegrator (class in openmm.openmm)
LangevinMiddleIntegrator (class in openmm.openmm)
linkedContextCreated() (openmm.openmm.Platform method)
loadBondDefinitions() (openmm.app.topology.Topology static method)
loadCheckpoint() (openmm.app.simulation.Simulation method)
(openmm.openmm.Context method)
loadFile() (openmm.app.forcefield.ForceField method)
loadHydrogenDefinitions() (openmm.app.modeller.Modeller static method)
loadParameters() (openmm.app.charmmpsffile.CharmmPsfFile method)
loadPluginLibrary() (openmm.openmm.Platform static method)
loadPluginsFromDirectory() (openmm.openmm.Platform static method)
loadSet() (openmm.app.charmmparameterset.CharmmParameterSet class method)
loadState() (openmm.app.simulation.Simulation method)
LocalCoordinatesSite (class in openmm.openmm)
LocalEnergyMinimizer (class in openmm.openmm)
M
max() (openmm.unit.quantity.Quantity method)
mean() (openmm.unit.quantity.Quantity method)
Metadynamics (class in openmm.app.metadynamics)
min() (openmm.unit.quantity.Quantity method)
minimize() (openmm.openmm.LocalEnergyMinimizer static method)
minimizeEnergy() (openmm.app.simulation.Simulation method)
Modeller (class in openmm.app.modeller)
MonteCarloAnisotropicBarostat (class in openmm.openmm)
MonteCarloBarostat (class in openmm.openmm)
MonteCarloFlexibleBarostat (class in openmm.openmm)
MonteCarloMembraneBarostat (class in openmm.openmm)
MTSIntegrator (class in openmm.mtsintegrator)
MTSLangevinIntegrator (class in openmm.mtsintegrator)
N
natom (openmm.app.charmmcrdfiles.CharmmCrdFile attribute)
(openmm.app.charmmcrdfiles.CharmmRstFile attribute)
NonbondedForce (class in openmm.openmm)
NoseHooverChain (class in openmm.openmm)
NoseHooverIntegrator (class in openmm.openmm)
O
OpenMMException (class in openmm)
OutOfPlaneSite (class in openmm.openmm)
P
PDBFile (class in openmm.app.pdbfile)
PDBReporter (class in openmm.app.pdbreporter)
PDBxFile (class in openmm.app.pdbxfile)
PDBxReporter (class in openmm.app.pdbreporter)
PeriodicTorsionForce (class in openmm.openmm)
Platform (class in openmm.openmm)
positions (openmm.app.charmmcrdfiles.CharmmCrdFile attribute)
(openmm.app.charmmcrdfiles.CharmmRstFile attribute)
positionsold (openmm.app.charmmcrdfiles.CharmmRstFile attribute)
Pressure() (openmm.openmm.MonteCarloBarostat static method)
(openmm.openmm.MonteCarloFlexibleBarostat static method)
(openmm.openmm.MonteCarloMembraneBarostat static method)
(openmm.openmm.RPMDMonteCarloBarostat static method)
PressureX() (openmm.openmm.MonteCarloAnisotropicBarostat static method)
PressureY() (openmm.openmm.MonteCarloAnisotropicBarostat static method)
PressureZ() (openmm.openmm.MonteCarloAnisotropicBarostat static method)
Q
Quantity (class in openmm.unit.quantity)
R
RBTorsionForce (class in openmm.openmm)
readParameterFile() (openmm.app.charmmparameterset.CharmmParameterSet method)
readStreamFile() (openmm.app.charmmparameterset.CharmmParameterSet method)
readTopologyFile() (openmm.app.charmmparameterset.CharmmParameterSet method)
reduce_unit() (openmm.unit.quantity.Quantity method)
registerAtomType() (openmm.app.forcefield.ForceField method)
registerGenerator() (openmm.app.forcefield.ForceField method)
registerPatch() (openmm.app.forcefield.ForceField method)
registerPlatform() (openmm.openmm.Platform static method)
registerProxy() (openmm.openmm.SerializationProxy static method)
registerResidueTemplate() (openmm.app.forcefield.ForceField method)
registerScript() (openmm.app.forcefield.ForceField method)
registerTemplateGenerator() (openmm.app.forcefield.ForceField method)
registerTemplateMatcher() (openmm.app.forcefield.ForceField method)
registerTemplatePatch() (openmm.app.forcefield.ForceField method)
reinitialize() (openmm.openmm.Context method)
removeConstraint() (openmm.openmm.System method)
removeForce() (openmm.openmm.System method)
report() (openmm.app.checkpointreporter.CheckpointReporter method)
(openmm.app.dcdreporter.DCDReporter method)
(openmm.app.pdbreporter.PDBReporter method)
(openmm.app.pdbreporter.PDBxReporter method)
(openmm.app.statedatareporter.StateDataReporter method)
reshape() (openmm.unit.quantity.Quantity method)
Residue (class in openmm.app.topology)
residues() (openmm.app.topology.Chain method)
(openmm.app.topology.Topology method)
resname (openmm.app.charmmcrdfiles.CharmmCrdFile attribute)
(openmm.app.charmmcrdfiles.CharmmRstFile attribute)
RMSDForce (class in openmm.openmm)
RPMDIntegrator (class in openmm.openmm)
RPMDMonteCarloBarostat (class in openmm.openmm)
runForClockTime() (openmm.app.simulation.Simulation method)
S
saveCheckpoint() (openmm.app.simulation.Simulation method)
saveState() (openmm.app.simulation.Simulation method)
ScaledUnit (class in openmm.unit.unit)
SerializationNode (class in openmm.openmm)
SerializationProxy (class in openmm.openmm)
serialize() (openmm.openmm.SerializationProxy method)
(openmm.openmm.XmlSerializer static method)
serializeSystem() (openmm.openmm.XmlSerializer static method)
setAcceptorParameters() (openmm.openmm.CustomHbondForce method)
setAEwald() (openmm.openmm.AmoebaMultipoleForce method)
setAlchemicalMethod() (openmm.openmm.AmoebaVdwForce method)
setAlpha() (openmm.amd.AMDIntegrator method)
setAlphaGroup() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.DualAMDIntegrator method)
setAlphaTotal() (openmm.amd.DualAMDIntegrator method)
setAngleParameters() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.HarmonicAngleForce method)
setApplyThermostat() (openmm.openmm.RPMDIntegrator method)
setAwater() (openmm.openmm.AmoebaWcaDispersionForce method)
setBondParameters() (openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.HarmonicBondForce method)
setBoolProperty() (openmm.openmm.SerializationNode method)
setBox() (openmm.app.charmmpsffile.CharmmPsfFile method)
setCollisionFrequency() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.NoseHooverIntegrator method)
setComputedValueParameters() (openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomNonbondedForce method)
setConstraintParameters() (openmm.openmm.System method)
setConstraintTolerance() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CompoundIntegrator method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.Integrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
(openmm.openmm.VerletIntegrator method)
setCovalentMap() (openmm.openmm.AmoebaMultipoleForce method)
setCurrentIntegrator() (openmm.openmm.CompoundIntegrator method)
setCutoff() (openmm.openmm.AmoebaVdwForce method)
setCutoffDistance() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
setDefaultCollisionFrequency() (openmm.openmm.AndersenThermostat method)
setDefaultPeriodicBoxVectors() (openmm.openmm.System method)
setDefaultPressure() (openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.RPMDMonteCarloBarostat method)
setDefaultSurfaceTension() (openmm.openmm.MonteCarloMembraneBarostat method)
setDefaultTemperature() (openmm.openmm.AndersenThermostat method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
setDispoff() (openmm.openmm.AmoebaWcaDispersionForce method)
setDonorParameters() (openmm.openmm.CustomHbondForce method)
setDoubleProperty() (openmm.openmm.SerializationNode method)
setDPMEParameters() (openmm.openmm.HippoNonbondedForce method)
setDrudeFriction() (openmm.openmm.DrudeLangevinIntegrator method)
setDrudeTemperature() (openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
setE() (openmm.amd.AMDIntegrator method)
setEGroup() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.DualAMDIntegrator method)
setEnergyFunction() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
setEnergyTermParameters() (openmm.openmm.CustomGBForce method)
setEpsh() (openmm.openmm.AmoebaWcaDispersionForce method)
setEpsilonCombiningRule() (openmm.openmm.AmoebaVdwForce method)
setEpso() (openmm.openmm.AmoebaWcaDispersionForce method)
setErrorTolerance() (openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
setETotal() (openmm.amd.DualAMDIntegrator method)
setEwaldErrorTolerance() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
setExceptionParameterOffset() (openmm.openmm.NonbondedForce method)
setExceptionParameters() (openmm.openmm.GayBerneForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
setExceptionsUsePeriodicBoundaryConditions() (openmm.openmm.NonbondedForce method)
setExclusionParticles() (openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
setExtrapolationCoefficients() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.HippoNonbondedForce method)
setForceGroup() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaTorsionTorsionForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.AndersenThermostat method)
(openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CMMotionRemover method)
(openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.Force method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HarmonicAngleForce method)
(openmm.openmm.HarmonicBondForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.NonbondedForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
(openmm.openmm.RMSDForce method)
(openmm.openmm.RPMDMonteCarloBarostat method)
setFrequency() (openmm.openmm.CMMotionRemover method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.RPMDMonteCarloBarostat method)
setFriction() (openmm.openmm.BrownianIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
setFunctionParameters() (openmm.openmm.Continuous1DFunction method)
(openmm.openmm.Continuous2DFunction method)
(openmm.openmm.Continuous3DFunction method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.Discrete1DFunction method)
(openmm.openmm.Discrete2DFunction method)
(openmm.openmm.Discrete3DFunction method)
setGlobalParameterDefaultValue() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.NonbondedForce method)
setGlobalParameterName() (openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.NonbondedForce method)
setGlobalVariable() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
setGlobalVariableByName() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
setGroupParameters() (openmm.openmm.CustomCentroidBondForce method)
setIncludeCavityTerm() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
setIncludeDirectSpace() (openmm.openmm.NonbondedForce method)
setIntegrationForceGroups() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CompoundIntegrator method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.Integrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
(openmm.openmm.VerletIntegrator method)
setInteractionGroupParameters() (openmm.openmm.CustomNonbondedForce method)
setIntProperty() (openmm.openmm.SerializationNode method)
setKineticEnergyExpression() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
setLJPMEParameters() (openmm.openmm.NonbondedForce method)
setLongProperty() (openmm.openmm.SerializationNode method)
setMapParameters() (openmm.openmm.CMAPTorsionForce method)
setMaxDrudeDistance() (openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
setMaximumPairDistance() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
setMaximumStepSize() (openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
setMinimizationErrorTolerance() (openmm.openmm.DrudeSCFIntegrator method)
setMultipoleParameters() (openmm.openmm.AmoebaMultipoleForce method)
setMutualInducedMaxIterations() (openmm.openmm.AmoebaMultipoleForce method)
setMutualInducedTargetEpsilon() (openmm.openmm.AmoebaMultipoleForce method)
setName() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaTorsionTorsionForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.AndersenThermostat method)
(openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CMMotionRemover method)
(openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.Force method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HarmonicAngleForce method)
(openmm.openmm.HarmonicBondForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.NonbondedForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
(openmm.openmm.RMSDForce method)
(openmm.openmm.RPMDMonteCarloBarostat method)
(openmm.openmm.SerializationNode method)
setNonbondedMethod() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
setNumDegreesOfFreedom() (openmm.openmm.NoseHooverChain method)
setParameter() (openmm.openmm.Context method)
setParticleExclusions() (openmm.openmm.AmoebaVdwForce method)
setParticleMass() (openmm.openmm.System method)
setParticleParameterOffset() (openmm.openmm.NonbondedForce method)
setParticleParameters() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
setParticles() (openmm.openmm.RMSDForce method)
setParticleTypeParameters() (openmm.openmm.AmoebaVdwForce method)
setPerAcceptorParameterName() (openmm.openmm.CustomHbondForce method)
setPerAngleParameterName() (openmm.openmm.CustomAngleForce method)
setPerBondParameterName() (openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
setPerDofVariable() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
setPerDofVariableByName() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.CustomIntegrator method)
setPerDonorParameterName() (openmm.openmm.CustomHbondForce method)
setPeriodicBoxVectors() (openmm.app.topology.Topology method)
(openmm.openmm.Context method)
setPermutationMode() (openmm.openmm.CustomManyParticleForce method)
setPerParticleParameterName() (openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
setPerTorsionParameterName() (openmm.openmm.CustomTorsionForce method)
setPmeGridDimensions() (openmm.openmm.AmoebaMultipoleForce method)
setPMEParameters() (openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
setPolarizationType() (openmm.openmm.AmoebaMultipoleForce method)
setPositions() (openmm.app.desmonddmsfile.DesmondDMSFile method)
(openmm.openmm.Context method)
(openmm.openmm.RPMDIntegrator method)
setPotentialFunction() (openmm.openmm.AmoebaVdwForce method)
setProbeRadius() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
setPropertyDefaultValue() (openmm.openmm.Platform method)
setPropertyValue() (openmm.openmm.Platform method)
setRandomNumberSeed() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.AndersenThermostat method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.RPMDMonteCarloBarostat method)
(openmm.openmm.VariableLangevinIntegrator method)
setReactionFieldDielectric() (openmm.openmm.NonbondedForce method)
setReciprocalSpaceForceGroup() (openmm.openmm.NonbondedForce method)
setReferencePositions() (openmm.openmm.RMSDForce method)
setRelativeCollisionFrequency() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.NoseHooverIntegrator method)
setRelativeTemperature() (openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.NoseHooverIntegrator method)
setRminh() (openmm.openmm.AmoebaWcaDispersionForce method)
setRmino() (openmm.openmm.AmoebaWcaDispersionForce method)
setScaleMoleculesAsRigid() (openmm.openmm.MonteCarloFlexibleBarostat method)
setScreenedPairParameters() (openmm.openmm.DrudeForce method)
setShctd() (openmm.openmm.AmoebaWcaDispersionForce method)
setSigmaCombiningRule() (openmm.openmm.AmoebaVdwForce method)
setSlevy() (openmm.openmm.AmoebaWcaDispersionForce method)
setSoftcoreAlpha() (openmm.openmm.AmoebaVdwForce method)
setSoftcorePower() (openmm.openmm.AmoebaVdwForce method)
setSoluteDielectric() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.GBSAOBCForce method)
setSolventDielectric() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.GBSAOBCForce method)
setState() (openmm.openmm.Context method)
setStepCount() (openmm.openmm.Context method)
setStepSize() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CompoundIntegrator method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.Integrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
(openmm.openmm.VerletIntegrator method)
setStringProperty() (openmm.openmm.SerializationNode method)
setSurfaceAreaEnergy() (openmm.openmm.GBSAOBCForce method)
setSurfaceAreaFactor() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
setSwitchingDistance() (openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
setTemperature() (openmm.openmm.BrownianIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
setThermostatedAtoms() (openmm.openmm.NoseHooverChain method)
setThermostatedPairs() (openmm.openmm.NoseHooverChain method)
setTime() (openmm.openmm.Context method)
setTorsionParameters() (openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
setTorsionTorsionGrid() (openmm.openmm.AmoebaTorsionTorsionForce method)
setTorsionTorsionParameters() (openmm.openmm.AmoebaTorsionTorsionForce method)
setTypeFilter() (openmm.openmm.CustomManyParticleForce method)
setTypePairParameters() (openmm.openmm.AmoebaVdwForce method)
setUnitCellDimensions() (openmm.app.topology.Topology method)
setUseDispersionCorrection() (openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.NonbondedForce method)
setUseLongRangeCorrection() (openmm.openmm.CustomNonbondedForce method)
setUsesPeriodicBoundaryConditions() (openmm.openmm.AmoebaTorsionTorsionForce method)
(openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.HarmonicAngleForce method)
(openmm.openmm.HarmonicBondForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
setUseSwitchingFunction() (openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.NonbondedForce method)
setVelocities() (openmm.app.desmonddmsfile.DesmondDMSFile method)
(openmm.openmm.Context method)
(openmm.openmm.RPMDIntegrator method)
setVelocitiesToTemperature() (openmm.openmm.Context method)
setVirtualSite() (openmm.openmm.System method)
setXYMode() (openmm.openmm.MonteCarloMembraneBarostat method)
setZMode() (openmm.openmm.MonteCarloMembraneBarostat method)
SimulatedTempering (class in openmm.app.simulatedtempering)
Simulation (class in openmm.app.simulation)
SiPrefix (class in openmm.unit.prefix)
sqrt() (openmm.unit.quantity.Quantity method)
(openmm.unit.unit.Unit method)
State (class in openmm.openmm)
StateDataReporter (class in openmm.app.statedatareporter)
std() (openmm.unit.quantity.Quantity method)
step() (openmm.amd.AMDForceGroupIntegrator method)
(openmm.amd.AMDIntegrator method)
(openmm.amd.DualAMDIntegrator method)
(openmm.app.metadynamics.Metadynamics method)
(openmm.app.simulatedtempering.SimulatedTempering method)
(openmm.app.simulation.Simulation method)
(openmm.mtsintegrator.MTSIntegrator method)
(openmm.mtsintegrator.MTSLangevinIntegrator method)
(openmm.openmm.BrownianIntegrator method)
(openmm.openmm.CompoundIntegrator method)
(openmm.openmm.CustomIntegrator method)
(openmm.openmm.DrudeIntegrator method)
(openmm.openmm.DrudeLangevinIntegrator method)
(openmm.openmm.DrudeNoseHooverIntegrator method)
(openmm.openmm.DrudeSCFIntegrator method)
(openmm.openmm.Integrator method)
(openmm.openmm.LangevinIntegrator method)
(openmm.openmm.LangevinMiddleIntegrator method)
(openmm.openmm.NoseHooverIntegrator method)
(openmm.openmm.RPMDIntegrator method)
(openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
(openmm.openmm.VerletIntegrator method)
stepTo() (openmm.openmm.VariableLangevinIntegrator method)
(openmm.openmm.VariableVerletIntegrator method)
sum() (openmm.unit.quantity.Quantity method)
supportsDoublePrecision() (openmm.openmm.Platform method)
supportsKernels() (openmm.openmm.Platform method)
SurfaceTension() (openmm.openmm.MonteCarloMembraneBarostat static method)
System (class in openmm.openmm)
system (openmm.app.charmmpsffile.CharmmPsfFile property)
T
TabulatedFunction (class in openmm.openmm)
Temperature() (openmm.openmm.AndersenThermostat static method)
(openmm.openmm.MonteCarloAnisotropicBarostat static method)
(openmm.openmm.MonteCarloBarostat static method)
(openmm.openmm.MonteCarloFlexibleBarostat static method)
(openmm.openmm.MonteCarloMembraneBarostat static method)
thisown (openmm.amd.AMDForceGroupIntegrator property)
(openmm.amd.AMDIntegrator property)
(openmm.amd.DualAMDIntegrator property)
(openmm.mtsintegrator.MTSIntegrator property)
(openmm.mtsintegrator.MTSLangevinIntegrator property)
(openmm.openmm.AmoebaGeneralizedKirkwoodForce property)
(openmm.openmm.AmoebaMultipoleForce property)
(openmm.openmm.AmoebaTorsionTorsionForce property)
(openmm.openmm.AmoebaVdwForce property)
(openmm.openmm.AmoebaWcaDispersionForce property)
(openmm.openmm.AndersenThermostat property)
(openmm.openmm.BrownianIntegrator property)
(openmm.openmm.CMAPTorsionForce property)
(openmm.openmm.CMMotionRemover property)
(openmm.openmm.CompoundIntegrator property)
(openmm.openmm.Context property)
(openmm.openmm.Continuous1DFunction property)
(openmm.openmm.Continuous2DFunction property)
(openmm.openmm.Continuous3DFunction property)
(openmm.openmm.CustomAngleForce property)
(openmm.openmm.CustomBondForce property)
(openmm.openmm.CustomCentroidBondForce property)
(openmm.openmm.CustomCompoundBondForce property)
(openmm.openmm.CustomCVForce property)
(openmm.openmm.CustomExternalForce property)
(openmm.openmm.CustomGBForce property)
(openmm.openmm.CustomHbondForce property)
(openmm.openmm.CustomIntegrator property)
(openmm.openmm.CustomManyParticleForce property)
(openmm.openmm.CustomNonbondedForce property)
(openmm.openmm.CustomTorsionForce property)
(openmm.openmm.Discrete1DFunction property)
(openmm.openmm.Discrete2DFunction property)
(openmm.openmm.Discrete3DFunction property)
(openmm.openmm.DrudeForce property)
(openmm.openmm.DrudeIntegrator property)
(openmm.openmm.DrudeLangevinIntegrator property)
(openmm.openmm.DrudeNoseHooverIntegrator property)
(openmm.openmm.DrudeSCFIntegrator property)
(openmm.openmm.Force property)
(openmm.openmm.GayBerneForce property)
(openmm.openmm.GBSAOBCForce property)
(openmm.openmm.HarmonicAngleForce property)
(openmm.openmm.HarmonicBondForce property)
(openmm.openmm.HippoNonbondedForce property)
(openmm.openmm.Integrator property)
(openmm.openmm.LangevinIntegrator property)
(openmm.openmm.LangevinMiddleIntegrator property)
(openmm.openmm.LocalCoordinatesSite property)
(openmm.openmm.LocalEnergyMinimizer property)
(openmm.openmm.MonteCarloAnisotropicBarostat property)
(openmm.openmm.MonteCarloBarostat property)
(openmm.openmm.MonteCarloFlexibleBarostat property)
(openmm.openmm.MonteCarloMembraneBarostat property)
(openmm.openmm.NonbondedForce property)
(openmm.openmm.NoseHooverChain property)
(openmm.openmm.NoseHooverIntegrator property)
(openmm.openmm.OutOfPlaneSite property)
(openmm.openmm.PeriodicTorsionForce property)
(openmm.openmm.Platform property)
(openmm.openmm.RBTorsionForce property)
(openmm.openmm.RMSDForce property)
(openmm.openmm.RPMDIntegrator property)
(openmm.openmm.RPMDMonteCarloBarostat property)
(openmm.openmm.SerializationNode property)
(openmm.openmm.SerializationProxy property)
(openmm.openmm.State property)
(openmm.openmm.System property)
(openmm.openmm.TabulatedFunction property)
(openmm.openmm.ThreeParticleAverageSite property)
(openmm.openmm.TwoParticleAverageSite property)
(openmm.openmm.VariableLangevinIntegrator property)
(openmm.openmm.VariableVerletIntegrator property)
(openmm.openmm.VerletIntegrator property)
(openmm.openmm.VirtualSite property)
(openmm.openmm.XmlSerializer property)
ThreeParticleAverageSite (class in openmm.openmm)
Topology (class in openmm.app.topology)
topology (openmm.app.charmmpsffile.CharmmPsfFile property)
TwoParticleAverageSite (class in openmm.openmm)
U
Unit (class in openmm.unit.unit)
UnitSystem (class in openmm.unit.unit)
updateParametersInContext() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HarmonicAngleForce method)
(openmm.openmm.HarmonicBondForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.NonbondedForce method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
(openmm.openmm.RMSDForce method)
usesPeriodicBoundaryConditions() (openmm.openmm.AmoebaGeneralizedKirkwoodForce method)
(openmm.openmm.AmoebaMultipoleForce method)
(openmm.openmm.AmoebaTorsionTorsionForce method)
(openmm.openmm.AmoebaVdwForce method)
(openmm.openmm.AmoebaWcaDispersionForce method)
(openmm.openmm.AndersenThermostat method)
(openmm.openmm.CMAPTorsionForce method)
(openmm.openmm.CMMotionRemover method)
(openmm.openmm.CustomAngleForce method)
(openmm.openmm.CustomBondForce method)
(openmm.openmm.CustomCentroidBondForce method)
(openmm.openmm.CustomCompoundBondForce method)
(openmm.openmm.CustomCVForce method)
(openmm.openmm.CustomExternalForce method)
(openmm.openmm.CustomGBForce method)
(openmm.openmm.CustomHbondForce method)
(openmm.openmm.CustomManyParticleForce method)
(openmm.openmm.CustomNonbondedForce method)
(openmm.openmm.CustomTorsionForce method)
(openmm.openmm.DrudeForce method)
(openmm.openmm.Force method)
(openmm.openmm.GayBerneForce method)
(openmm.openmm.GBSAOBCForce method)
(openmm.openmm.HarmonicAngleForce method)
(openmm.openmm.HarmonicBondForce method)
(openmm.openmm.HippoNonbondedForce method)
(openmm.openmm.MonteCarloAnisotropicBarostat method)
(openmm.openmm.MonteCarloBarostat method)
(openmm.openmm.MonteCarloFlexibleBarostat method)
(openmm.openmm.MonteCarloMembraneBarostat method)
(openmm.openmm.NonbondedForce method)
(openmm.openmm.NoseHooverChain method)
(openmm.openmm.PeriodicTorsionForce method)
(openmm.openmm.RBTorsionForce method)
(openmm.openmm.RMSDForce method)
(openmm.openmm.RPMDMonteCarloBarostat method)
(openmm.openmm.System method)
V
value_in_unit() (openmm.unit.quantity.Quantity method)
value_in_unit_system() (openmm.unit.quantity.Quantity method)
VariableLangevinIntegrator (class in openmm.openmm)
VariableVerletIntegrator (class in openmm.openmm)
Vec3 (class in openmm.vec3)
velocities (openmm.app.charmmcrdfiles.CharmmRstFile attribute)
VerletIntegrator (class in openmm.openmm)
VirtualSite (class in openmm.openmm)
W
with_traceback() (openmm.app.internal.charmm.exceptions.CharmmPSFWarning method)
(openmm.OpenMMException method)
writeFile() (openmm.app.pdbfile.PDBFile static method)
(openmm.app.pdbxfile.PDBxFile static method)
writeFooter() (openmm.app.pdbfile.PDBFile static method)
writeHeader() (openmm.app.pdbfile.PDBFile static method)
(openmm.app.pdbxfile.PDBxFile static method)
writeModel() (openmm.app.dcdfile.DCDFile method)
(openmm.app.pdbfile.PDBFile static method)
(openmm.app.pdbxfile.PDBxFile static method)
X
x (openmm.vec3.Vec3 property)
XmlSerializer (class in openmm.openmm)
Y
y (openmm.vec3.Vec3 property)
Z
z (openmm.vec3.Vec3 property)
OpenMM Python API
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