- s -

• serializeSystem() : XmlSerializer
• setAcceptorParameters() : CustomHbondForce
• setAEwald() : AmoebaMultipoleForce
• setAmoebaGlobalHarmonicAngleCubic() : AmoebaHarmonicAngleForce
• setAmoebaGlobalHarmonicAnglePentic() : AmoebaHarmonicAngleForce
• setAmoebaGlobalHarmonicAngleQuartic() : AmoebaHarmonicAngleForce
• setAmoebaGlobalHarmonicAngleSextic() : AmoebaHarmonicAngleForce
• setAmoebaGlobalHarmonicBondCubic() : AmoebaHarmonicBondForce
• setAmoebaGlobalHarmonicBondQuartic() : AmoebaHarmonicBondForce
• setAmoebaGlobalHarmonicInPlaneAngleCubic() : AmoebaHarmonicInPlaneAngleForce
• setAmoebaGlobalHarmonicInPlaneAnglePentic() : AmoebaHarmonicInPlaneAngleForce
• setAmoebaGlobalHarmonicInPlaneAngleQuartic() : AmoebaHarmonicInPlaneAngleForce
• setAmoebaGlobalHarmonicInPlaneAngleSextic() : AmoebaHarmonicInPlaneAngleForce
• setAmoebaGlobalOutOfPlaneBendCubic() : AmoebaOutOfPlaneBendForce
• setAmoebaGlobalOutOfPlaneBendPentic() : AmoebaOutOfPlaneBendForce
• setAmoebaGlobalOutOfPlaneBendQuartic() : AmoebaOutOfPlaneBendForce
• setAmoebaGlobalOutOfPlaneBendSextic() : AmoebaOutOfPlaneBendForce
• setAmoebaGlobalUreyBradleyCubic() : AmoebaUreyBradleyForce
• setAmoebaGlobalUreyBradleyQuartic() : AmoebaUreyBradleyForce
• setAngleParameters() : AmoebaHarmonicAngleForce , AmoebaHarmonicInPlaneAngleForce , CustomAngleForce , HarmonicAngleForce
• setAwater() : AmoebaWcaDispersionForce
• setBondParameters() : AmoebaHarmonicBondForce , CustomBondForce , GBVIForce , GBVISoftcoreForce , HarmonicBondForce
• setBornRadiusScalingMethod() : GBVIForce , GBVISoftcoreForce
• setComputedValueParameters() : CustomGBForce
• setConstraintParameters() : System
• setConstraintTolerance() : Integrator
• setCovalentMap() : AmoebaMultipoleForce
• setCutoff() : AmoebaVdwForce
• setCutoffDistance() : AmoebaMultipoleForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , GBSAOBCForce , GBSAOBCSoftcoreForce , GBVIForce , GBVISoftcoreForce , NonbondedForce , NonbondedSoftcoreForce
• setDefaultPeriodicBoxVectors() : System
• setDispoff() : AmoebaWcaDispersionForce
• setDonorParameters() : CustomHbondForce
• setEnergyFunction() : CustomAngleForce , CustomBondForce , CustomExternalForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce
• setEnergyTermParameters() : CustomGBForce
• setEpsh() : AmoebaWcaDispersionForce
• setEpsilonCombiningRule() : AmoebaVdwForce
• setEpso() : AmoebaWcaDispersionForce
• setErrorTolerance() : VariableLangevinIntegrator , VariableVerletIntegrator
• setEwaldErrorTolerance() : AmoebaMultipoleForce , NonbondedForce
• setExceptionParameters() : NonbondedForce , NonbondedSoftcoreForce
• setExclusionParticles() : CustomGBForce , CustomHbondForce , CustomNonbondedForce
• setForceGroup() : Force
• setFrequency() : CMMotionRemover , MonteCarloBarostat
• setFriction() : BrownianIntegrator , LangevinIntegrator , RPMDIntegrator , VariableLangevinIntegrator
• setFunctionParameters() : CustomGBForce , CustomHbondForce , CustomNonbondedForce
• setGlobalParameterDefaultValue() : CustomAngleForce , CustomBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce
• setGlobalParameterName() : CustomAngleForce , CustomBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce
• setGlobalVariable() : CustomIntegrator
• setGlobalVariableByName() : CustomIntegrator
• setIncludeCavityTerm() : AmoebaGeneralizedKirkwoodForce
• setMapParameters() : CMAPTorsionForce
• setMultipoleParameters() : AmoebaMultipoleForce
• setMutualInducedMaxIterations() : AmoebaMultipoleForce
• setMutualInducedTargetEpsilon() : AmoebaMultipoleForce
• setNonbondedMethod() : AmoebaMultipoleForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , GBSAOBCForce , GBSAOBCSoftcoreForce , GBVIForce , GBVISoftcoreForce , NonbondedForce , NonbondedSoftcoreForce
• setNonPolarPrefactor() : GBSAOBCSoftcoreForce
• setOutOfPlaneBendParameters() : AmoebaOutOfPlaneBendForce
• setParameter() : Context
• setParticleExclusions() : AmoebaVdwForce
• setParticleMass() : System
• setParticleParameters() : CustomGBForce , GBVIForce , AmoebaGeneralizedKirkwoodForce , AmoebaVdwForce , AmoebaWcaDispersionForce , CustomExternalForce , CustomNonbondedForce , GBSAOBCForce , GBSAOBCSoftcoreForce , GBVISoftcoreForce , NonbondedForce , NonbondedSoftcoreForce
• setPBC() : AmoebaVdwForce
• setPerAcceptorParameterName() : CustomHbondForce
• setPerAngleParameterName() : CustomAngleForce
• setPerBondParameterName() : CustomBondForce
• setPerDofVariable() : CustomIntegrator
• setPerDofVariableByName() : CustomIntegrator
• setPerDonorParameterName() : CustomHbondForce
• setPeriodicBoxVectors() : Context
• setPerParticleParameterName() : CustomExternalForce , CustomGBForce , CustomNonbondedForce
• setPerTorsionParameterName() : CustomTorsionForce
• setPiTorsionParameters() : AmoebaPiTorsionForce
• setPmeGridDimensions() : AmoebaMultipoleForce
• setPolarizationType() : AmoebaMultipoleForce
• setPositions() : Context , RPMDIntegrator
• setProbeRadius() : AmoebaGeneralizedKirkwoodForce
• setPropertyDefaultValue() : Platform
• setPropertyValue() : Platform
• setQuinticLowerLimitFactor() : GBVIForce , GBVISoftcoreForce
• setQuinticUpperBornRadiusLimit() : GBVIForce , GBVISoftcoreForce
• setRandomNumberSeed() : BrownianIntegrator , LangevinIntegrator , RPMDIntegrator , CustomIntegrator , VariableLangevinIntegrator , AndersenThermostat , MonteCarloBarostat
• setReactionFieldDielectric() : NonbondedForce , NonbondedSoftcoreForce
• setReciprocalSpaceForceGroup() : NonbondedForce
• setRminh() : AmoebaWcaDispersionForce
• setRmino() : AmoebaWcaDispersionForce
• setShctd() : AmoebaWcaDispersionForce
• setSigmaCombiningRule() : AmoebaVdwForce
• setSlevy() : AmoebaWcaDispersionForce
• setSoluteDielectric() : GBSAOBCForce , AmoebaGeneralizedKirkwoodForce , GBSAOBCSoftcoreForce , GBVISoftcoreForce , GBVIForce
• setSolventDielectric() : GBVISoftcoreForce , GBVIForce , AmoebaGeneralizedKirkwoodForce , GBSAOBCSoftcoreForce , GBSAOBCForce
• setStepSize() : Integrator
• setStretchBendParameters() : AmoebaStretchBendForce
• setSurfaceAreaFactor() : AmoebaGeneralizedKirkwoodForce
• setTemperature() : MonteCarloBarostat , BrownianIntegrator , VariableLangevinIntegrator , RPMDIntegrator , LangevinIntegrator
• setTime() : Context
• setTorsionParameters() : CMAPTorsionForce , CustomTorsionForce , RBTorsionForce , PeriodicTorsionForce , AmoebaTorsionForce
• setTorsionTorsionGrid() : AmoebaTorsionTorsionForce
• setTorsionTorsionParameters() : AmoebaTorsionTorsionForce
• setUnitCellDimensions() : Topology
• setUreyBradleyParameters() : AmoebaUreyBradleyForce
• setUseDispersionCorrection() : NonbondedForce
• setUseNeighborList() : AmoebaVdwForce
• setVelocities() : RPMDIntegrator , Context
• setVirtualSite() : System
• step() : VariableVerletIntegrator , Integrator , BrownianIntegrator , Simulation , VerletIntegrator , CustomIntegrator , LangevinIntegrator , RPMDIntegrator , VariableLangevinIntegrator
• stepTo() : VariableLangevinIntegrator , VariableVerletIntegrator
• supportsDoublePrecision() : Platform
• supportsKernels() : Platform