### - s -

- serialize() : XmlSerializer
- serializeSystem() : XmlSerializer
- setAcceptorParameters() : CustomHbondForce
- setAEwald() : AmoebaMultipoleForce
- 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() : CustomAngleForce , AmoebaInPlaneAngleForce , HarmonicAngleForce , AmoebaAngleForce
- setApplyThermostat() : RPMDIntegrator
- setAwater() : AmoebaWcaDispersionForce
- setBondParameters() : AmoebaBondForce , HarmonicBondForce , CustomBondForce , GBVIForce , CustomCompoundBondForce
- setBornRadiusScalingMethod() : GBVIForce
- setBox() : CharmmPsfFile
- setComputedValueParameters() : CustomGBForce
- setConstraintParameters() : System
- setConstraintTolerance() : Integrator
- setCovalentMap() : AmoebaMultipoleForce
- setCutoff() : AmoebaVdwForce
- setCutoffDistance() : CustomNonbondedForce , CustomHbondForce , NonbondedForce , CustomGBForce , GBVIForce , AmoebaMultipoleForce , GBSAOBCForce , CustomManyParticleForce
- setDefaultCollisionFrequency() : AndersenThermostat
- setDefaultPeriodicBoxVectors() : System
- setDefaultPressure() : MonteCarloAnisotropicBarostat , MonteCarloBarostat , MonteCarloMembraneBarostat
- setDefaultSurfaceTension() : MonteCarloMembraneBarostat
- setDefaultTemperature() : AndersenThermostat
- setDispoff() : AmoebaWcaDispersionForce
- setDonorParameters() : CustomHbondForce
- setDrudeFriction() : DrudeLangevinIntegrator
- setDrudeTemperature() : DrudeLangevinIntegrator
- setEnergyFunction() : CustomAngleForce , CustomExternalForce , CustomTorsionForce , CustomNonbondedForce , CustomHbondForce , CustomBondForce , CustomCompoundBondForce , CustomManyParticleForce
- setEnergyTermParameters() : CustomGBForce
- setEpsh() : AmoebaWcaDispersionForce
- setEpsilonCombiningRule() : AmoebaVdwForce
- setEpso() : AmoebaWcaDispersionForce
- setErrorTolerance() : VariableVerletIntegrator , VariableLangevinIntegrator
- setEwaldErrorTolerance() : NonbondedForce , AmoebaMultipoleForce
- setExceptionParameters() : NonbondedForce
- setExclusionParticles() : CustomNonbondedForce , CustomHbondForce , CustomGBForce , CustomManyParticleForce
- setForceGroup() : Force
- setFrequency() : MonteCarloAnisotropicBarostat , MonteCarloBarostat , MonteCarloMembraneBarostat , CMMotionRemover
- setFriction() : DrudeLangevinIntegrator , RPMDIntegrator , VariableLangevinIntegrator , BrownianIntegrator , LangevinIntegrator
- setFunctionParameters() : Discrete3DFunction , Continuous3DFunction , CustomNonbondedForce , CustomHbondForce , Continuous1DFunction , CustomGBForce , Continuous2DFunction , Discrete2DFunction , CustomCompoundBondForce , Discrete1DFunction
- setGlobalParameterDefaultValue() : CustomAngleForce , CustomExternalForce , CustomTorsionForce , CustomNonbondedForce , CustomHbondForce , CustomBondForce , CustomGBForce , CustomCompoundBondForce , CustomManyParticleForce
- setGlobalParameterName() : CustomAngleForce , CustomExternalForce , CustomTorsionForce , CustomNonbondedForce , CustomHbondForce , CustomBondForce , CustomGBForce , CustomCompoundBondForce , CustomManyParticleForce
- setGlobalVariable() : CustomIntegrator
- setGlobalVariableByName() : CustomIntegrator
- setIncludeCavityTerm() : AmoebaGeneralizedKirkwoodForce
- setInteractionGroupParameters() : CustomNonbondedForce
- setKineticEnergyExpression() : CustomIntegrator
- setMapParameters() : CMAPTorsionForce
- setMinimizationErrorTolerance() : DrudeSCFIntegrator
- setMultipoleParameters() : AmoebaMultipoleForce
- setMutualInducedMaxIterations() : AmoebaMultipoleForce
- setMutualInducedTargetEpsilon() : AmoebaMultipoleForce
- setNonbondedMethod() : CustomGBForce , GBVIForce , AmoebaMultipoleForce , AmoebaVdwForce , GBSAOBCForce , CustomManyParticleForce , CustomNonbondedForce , CustomHbondForce , NonbondedForce
- setOutOfPlaneBendParameters() : AmoebaOutOfPlaneBendForce
- setParameter() : Context
- setParticleExclusions() : AmoebaVdwForce
- setParticleMass() : System
- setParticleParameters() : CustomExternalForce , CustomNonbondedForce , NonbondedForce , CustomGBForce , DrudeForce , AmoebaWcaDispersionForce , AmoebaVdwForce , GBSAOBCForce , CustomManyParticleForce , GBVIForce , AmoebaGeneralizedKirkwoodForce
- setPerAcceptorParameterName() : CustomHbondForce
- setPerAngleParameterName() : CustomAngleForce
- setPerBondParameterName() : CustomCompoundBondForce , CustomBondForce
- setPerDofVariable() : CustomIntegrator
- setPerDofVariableByName() : CustomIntegrator
- setPerDonorParameterName() : CustomHbondForce
- setPeriodicBoxVectors() : 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 , CustomIntegrator , VariableLangevinIntegrator , MonteCarloBarostat , RPMDIntegrator , DrudeLangevinIntegrator , MonteCarloMembraneBarostat , BrownianIntegrator , LangevinIntegrator , MonteCarloAnisotropicBarostat
- setReactionFieldDielectric() : NonbondedForce
- setReciprocalSpaceForceGroup() : NonbondedForce
- setRminh() : AmoebaWcaDispersionForce
- setRmino() : AmoebaWcaDispersionForce
- setScreenedPairParameters() : DrudeForce
- setShctd() : AmoebaWcaDispersionForce
- setSigmaCombiningRule() : AmoebaVdwForce
- setSlevy() : AmoebaWcaDispersionForce
- setSoluteDielectric() : AmoebaGeneralizedKirkwoodForce , GBVIForce , GBSAOBCForce
- setSolventDielectric() : GBVIForce , AmoebaGeneralizedKirkwoodForce , GBSAOBCForce
- setState() : Context
- setStepSize() : Integrator
- setStretchBendParameters() : AmoebaStretchBendForce
- setSurfaceAreaEnergy() : GBSAOBCForce
- setSurfaceAreaFactor() : AmoebaGeneralizedKirkwoodForce
- setSwitchingDistance() : NonbondedForce , CustomNonbondedForce
- setTemperature() : VariableLangevinIntegrator , MonteCarloBarostat , BrownianIntegrator , MonteCarloMembraneBarostat , DrudeLangevinIntegrator , LangevinIntegrator , MonteCarloAnisotropicBarostat , RPMDIntegrator
- setTime() : Context
- setTorsionParameters() : CustomTorsionForce , RBTorsionForce , CMAPTorsionForce , PeriodicTorsionForce
- setTorsionTorsionGrid() : AmoebaTorsionTorsionForce
- setTorsionTorsionParameters() : AmoebaTorsionTorsionForce
- setTypeFilter() : CustomManyParticleForce
- setUnitCellDimensions() : Topology
- setUseDispersionCorrection() : NonbondedForce , AmoebaVdwForce
- setUseLongRangeCorrection() : CustomNonbondedForce
- setUseSwitchingFunction() : NonbondedForce , CustomNonbondedForce
- setVelocities() : Context , RPMDIntegrator
- setVelocitiesToTemperature() : Context
- setVirtualSite() : System
- setXYMode() : MonteCarloMembraneBarostat
- setZMode() : MonteCarloMembraneBarostat
- step() : LangevinIntegrator , VariableLangevinIntegrator , Simulation , Integrator , CustomIntegrator , VerletIntegrator , DrudeLangevinIntegrator , RPMDIntegrator , BrownianIntegrator , DrudeSCFIntegrator , VariableVerletIntegrator
- stepTo() : VariableVerletIntegrator , VariableLangevinIntegrator
- supportsDoublePrecision() : Platform
- supportsKernels() : Platform
- SurfaceTension() : MonteCarloMembraneBarostat
- symbol() : Element
- system() : CharmmPsfFile