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All Classes Namespaces Functions Variables Pages
Here is a list of all class members with links to the classes they belong to:

### - s -

- saveCheckpoint() : Simulation
- saveState() : Simulation
- segid : CharmmCrdFile
- serialize() : XmlSerializer
- serializeSystem() : XmlSerializer
- setAcceptorParameters() : CustomHbondForce
- setAEwald() : AmoebaMultipoleForce
- setAlpha() : AMDIntegrator
- setAlphaGroup() : AMDForceGroupIntegrator , DualAMDIntegrator
- setAlphaTotal() : DualAMDIntegrator
- setAmoebaGlobalAngleCubic() : AmoebaAngleForce
- setAmoebaGlobalAnglePentic() : AmoebaAngleForce
- setAmoebaGlobalAngleQuartic() : AmoebaAngleForce
- setAmoebaGlobalAngleSextic() : AmoebaAngleForce
- setAmoebaGlobalBondCubic() : AmoebaBondForce
- setAmoebaGlobalBondQuartic() : AmoebaBondForce
- setAmoebaGlobalInPlaneAngleCubic() : AmoebaInPlaneAngleForce
- setAmoebaGlobalInPlaneAnglePentic() : AmoebaInPlaneAngleForce
- setAmoebaGlobalInPlaneAngleQuartic() : AmoebaInPlaneAngleForce
- setAmoebaGlobalInPlaneAngleSextic() : AmoebaInPlaneAngleForce
- setAmoebaGlobalOutOfPlaneBendCubic() : AmoebaOutOfPlaneBendForce
- setAmoebaGlobalOutOfPlaneBendPentic() : AmoebaOutOfPlaneBendForce
- setAmoebaGlobalOutOfPlaneBendQuartic() : AmoebaOutOfPlaneBendForce
- setAmoebaGlobalOutOfPlaneBendSextic() : AmoebaOutOfPlaneBendForce
- setAngleParameters() : AmoebaAngleForce , AmoebaInPlaneAngleForce , CustomAngleForce , HarmonicAngleForce
- setApplyThermostat() : RPMDIntegrator
- setAwater() : AmoebaWcaDispersionForce
- setBondParameters() : AmoebaBondForce , CustomBondForce , CustomCompoundBondForce , GBVIForce , HarmonicBondForce
- setBornRadiusScalingMethod() : GBVIForce
- setBox() : CharmmPsfFile
- setComputedValueParameters() : CustomGBForce
- setConstraintParameters() : System
- setConstraintTolerance() : Integrator
- setCovalentMap() : AmoebaMultipoleForce
- setCutoff() : AmoebaVdwForce
- setCutoffDistance() : AmoebaMultipoleForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce
- setDefaultCollisionFrequency() : AndersenThermostat
- setDefaultPeriodicBoxVectors() : System
- setDefaultPressure() : MonteCarloAnisotropicBarostat , MonteCarloBarostat , MonteCarloMembraneBarostat , RPMDMonteCarloBarostat
- setDefaultSurfaceTension() : MonteCarloMembraneBarostat
- setDefaultTemperature() : AndersenThermostat
- setDispoff() : AmoebaWcaDispersionForce
- setDonorParameters() : CustomHbondForce
- setDrudeFriction() : DrudeLangevinIntegrator
- setDrudeTemperature() : DrudeLangevinIntegrator
- setE() : AMDIntegrator
- setEGroup() : AMDForceGroupIntegrator , DualAMDIntegrator
- setEnergyFunction() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , CustomTorsionForce
- setEnergyTermParameters() : CustomGBForce
- setEpsh() : AmoebaWcaDispersionForce
- setEpsilonCombiningRule() : AmoebaVdwForce
- setEpso() : AmoebaWcaDispersionForce
- setErrorTolerance() : VariableLangevinIntegrator , VariableVerletIntegrator
- setETotal() : DualAMDIntegrator
- setEwaldErrorTolerance() : AmoebaMultipoleForce , NonbondedForce
- setExceptionParameters() : NonbondedForce
- setExclusionParticles() : CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce
- setForceGroup() : Force
- setFrequency() : CMMotionRemover , MonteCarloAnisotropicBarostat , MonteCarloBarostat , MonteCarloMembraneBarostat , RPMDMonteCarloBarostat
- setFriction() : BrownianIntegrator , DrudeLangevinIntegrator , LangevinIntegrator , RPMDIntegrator , VariableLangevinIntegrator
- setFunctionParameters() : Continuous1DFunction , Continuous2DFunction , Continuous3DFunction , CustomCompoundBondForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , Discrete1DFunction , Discrete2DFunction , Discrete3DFunction
- setGlobalParameterDefaultValue() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , CustomTorsionForce
- setGlobalParameterName() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , CustomTorsionForce
- setGlobalVariable() : CustomIntegrator
- setGlobalVariableByName() : CustomIntegrator
- setIncludeCavityTerm() : AmoebaGeneralizedKirkwoodForce
- setInteractionGroupParameters() : CustomNonbondedForce
- setKineticEnergyExpression() : CustomIntegrator
- setMapParameters() : CMAPTorsionForce
- setMinimizationErrorTolerance() : DrudeSCFIntegrator
- setMultipoleParameters() : AmoebaMultipoleForce
- setMutualInducedMaxIterations() : AmoebaMultipoleForce
- setMutualInducedTargetEpsilon() : AmoebaMultipoleForce
- setNonbondedMethod() : AmoebaMultipoleForce , AmoebaVdwForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce
- setOutOfPlaneBendParameters() : AmoebaOutOfPlaneBendForce
- setParameter() : Context
- setParticleExclusions() : AmoebaVdwForce
- setParticleMass() : System
- setParticleParameters() : AmoebaGeneralizedKirkwoodForce , AmoebaVdwForce , AmoebaWcaDispersionForce , CustomExternalForce , CustomGBForce , CustomManyParticleForce , CustomNonbondedForce , DrudeForce , GBSAOBCForce , GBVIForce , NonbondedForce
- setPerAcceptorParameterName() : CustomHbondForce
- setPerAngleParameterName() : CustomAngleForce
- setPerBondParameterName() : CustomBondForce , CustomCompoundBondForce
- setPerDofVariable() : CustomIntegrator
- setPerDofVariableByName() : CustomIntegrator
- setPerDonorParameterName() : CustomHbondForce
- setPeriodicBoxVectors() : Topology , Context
- setPermutationMode() : CustomManyParticleForce
- setPerParticleParameterName() : CustomExternalForce , CustomGBForce , CustomManyParticleForce , CustomNonbondedForce
- setPerTorsionParameterName() : CustomTorsionForce
- setPiTorsionParameters() : AmoebaPiTorsionForce
- setPmeGridDimensions() : AmoebaMultipoleForce
- setPMEParameters() : NonbondedForce
- setPolarizationType() : AmoebaMultipoleForce
- setPositions() : Context , RPMDIntegrator
- setProbeRadius() : AmoebaGeneralizedKirkwoodForce
- setPropertyDefaultValue() : Platform
- setPropertyValue() : Platform
- setQuinticLowerLimitFactor() : GBVIForce
- setQuinticUpperBornRadiusLimit() : GBVIForce
- setRandomNumberSeed() : AndersenThermostat , BrownianIntegrator , CustomIntegrator , DrudeLangevinIntegrator , LangevinIntegrator , MonteCarloAnisotropicBarostat , MonteCarloBarostat , MonteCarloMembraneBarostat , RPMDIntegrator , RPMDMonteCarloBarostat , VariableLangevinIntegrator
- setReactionFieldDielectric() : NonbondedForce
- setReciprocalSpaceForceGroup() : NonbondedForce
- setRminh() : AmoebaWcaDispersionForce
- setRmino() : AmoebaWcaDispersionForce
- setScreenedPairParameters() : DrudeForce
- setShctd() : AmoebaWcaDispersionForce
- setSigmaCombiningRule() : AmoebaVdwForce
- setSlevy() : AmoebaWcaDispersionForce
- setSoluteDielectric() : AmoebaGeneralizedKirkwoodForce , GBSAOBCForce , GBVIForce
- setSolventDielectric() : AmoebaGeneralizedKirkwoodForce , GBSAOBCForce , GBVIForce
- setState() : Context
- setStepSize() : Integrator
- setStretchBendParameters() : AmoebaStretchBendForce
- setSurfaceAreaEnergy() : GBSAOBCForce
- setSurfaceAreaFactor() : AmoebaGeneralizedKirkwoodForce
- setSwitchingDistance() : CustomNonbondedForce , NonbondedForce
- setTemperature() : BrownianIntegrator , DrudeLangevinIntegrator , LangevinIntegrator , MonteCarloAnisotropicBarostat , MonteCarloBarostat , MonteCarloMembraneBarostat , RPMDIntegrator , VariableLangevinIntegrator
- setTime() : Context
- setTorsionParameters() : CMAPTorsionForce , CustomTorsionForce , PeriodicTorsionForce , RBTorsionForce
- setTorsionTorsionGrid() : AmoebaTorsionTorsionForce
- setTorsionTorsionParameters() : AmoebaTorsionTorsionForce
- setTypeFilter() : CustomManyParticleForce
- setUnitCellDimensions() : Topology
- setUseDispersionCorrection() : AmoebaVdwForce , NonbondedForce
- setUseLongRangeCorrection() : CustomNonbondedForce
- setUseSwitchingFunction() : CustomNonbondedForce , NonbondedForce
- setVelocities() : Context , RPMDIntegrator
- setVelocitiesToTemperature() : Context
- setVirtualSite() : System
- setXYMode() : MonteCarloMembraneBarostat
- setZMode() : MonteCarloMembraneBarostat
- SingleParticle : CustomGBForce
- SinglePermutation : CustomManyParticleForce
- step() : Simulation , BrownianIntegrator , CustomIntegrator , DrudeLangevinIntegrator , DrudeSCFIntegrator , Integrator , LangevinIntegrator , RPMDIntegrator , VariableLangevinIntegrator , VariableVerletIntegrator , VerletIntegrator
- stepTo() : VariableLangevinIntegrator , VariableVerletIntegrator
- supportsDoublePrecision() : Platform
- supportsKernels() : Platform
- SurfaceTension() : MonteCarloMembraneBarostat
- symbol() : Element
- system() : CharmmPsfFile , Simulation