- 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() : AmoebaAngleForce , AmoebaInPlaneAngleForce , CustomAngleForce , HarmonicAngleForce
• setAwater() : AmoebaWcaDispersionForce
• setBondParameters() : AmoebaBondForce , CustomBondForce , CustomCompoundBondForce , GBVIForce , HarmonicBondForce
• setBornRadiusScalingMethod() : GBVIForce
• setComputedValueParameters() : CustomGBForce
• setConstraintParameters() : System
• setConstraintTolerance() : Integrator
• setCovalentMap() : AmoebaMultipoleForce
• setCutoff() : AmoebaVdwForce
• setCutoffDistance() : AmoebaMultipoleForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce
• setDefaultPeriodicBoxVectors() : System
• setDispoff() : AmoebaWcaDispersionForce
• setDonorParameters() : CustomHbondForce
• setEnergyFunction() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce
• setEnergyTermParameters() : CustomGBForce
• setEpsh() : AmoebaWcaDispersionForce
• setEpsilonCombiningRule() : AmoebaVdwForce
• setEpso() : AmoebaWcaDispersionForce
• setErrorTolerance() : VariableLangevinIntegrator , VariableVerletIntegrator
• setEwaldErrorTolerance() : AmoebaMultipoleForce , NonbondedForce
• setExceptionParameters() : NonbondedForce
• setExclusionParticles() : CustomGBForce , CustomHbondForce , CustomNonbondedForce
• setForceGroup() : Force
• setFrequency() : CMMotionRemover , MonteCarloBarostat
• setFriction() : BrownianIntegrator , LangevinIntegrator , RPMDIntegrator , VariableLangevinIntegrator
• setFunctionParameters() : CustomCompoundBondForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce
• setGlobalParameterDefaultValue() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce
• setGlobalParameterName() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce
• setGlobalVariable() : CustomIntegrator
• setGlobalVariableByName() : CustomIntegrator
• setIncludeCavityTerm() : AmoebaGeneralizedKirkwoodForce
• setKineticEnergyExpression() : CustomIntegrator
• setMapParameters() : CMAPTorsionForce
• setMultipoleParameters() : AmoebaMultipoleForce
• setMutualInducedMaxIterations() : AmoebaMultipoleForce
• setMutualInducedTargetEpsilon() : AmoebaMultipoleForce
• setNonbondedMethod() : CustomNonbondedForce , AmoebaMultipoleForce , AmoebaVdwForce , CustomGBForce , CustomHbondForce , GBSAOBCForce , GBVIForce , NonbondedForce
• setOutOfPlaneBendParameters() : AmoebaOutOfPlaneBendForce
• setParameter() : Context
• setParticleExclusions() : AmoebaVdwForce
• setParticleMass() : System
• setParticleParameters() : NonbondedForce , AmoebaGeneralizedKirkwoodForce , AmoebaVdwForce , AmoebaWcaDispersionForce , CustomExternalForce , CustomGBForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce
• setPerAcceptorParameterName() : CustomHbondForce
• setPerAngleParameterName() : CustomAngleForce
• setPerBondParameterName() : CustomCompoundBondForce , 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
• setQuinticUpperBornRadiusLimit() : GBVIForce
• setRandomNumberSeed() : CustomIntegrator , LangevinIntegrator , VariableLangevinIntegrator , BrownianIntegrator , RPMDIntegrator , MonteCarloBarostat , AndersenThermostat
• setReactionFieldDielectric() : NonbondedForce
• setReciprocalSpaceForceGroup() : NonbondedForce
• setRminh() : AmoebaWcaDispersionForce
• setRmino() : AmoebaWcaDispersionForce
• setShctd() : AmoebaWcaDispersionForce
• setSigmaCombiningRule() : AmoebaVdwForce
• setSlevy() : AmoebaWcaDispersionForce
• setSoluteDielectric() : AmoebaGeneralizedKirkwoodForce , GBVIForce , GBSAOBCForce
• setSolventDielectric() : GBVIForce , AmoebaGeneralizedKirkwoodForce , GBSAOBCForce
• setState() : Context
• setStepSize() : Integrator
• setStretchBendParameters() : AmoebaStretchBendForce
• setSurfaceAreaFactor() : AmoebaGeneralizedKirkwoodForce
• setTemperature() : LangevinIntegrator , BrownianIntegrator , MonteCarloBarostat , RPMDIntegrator , VariableLangevinIntegrator
• setTime() : Context
• setTorsionParameters() : PeriodicTorsionForce , CustomTorsionForce , RBTorsionForce , CMAPTorsionForce
• setTorsionTorsionGrid() : AmoebaTorsionTorsionForce
• setTorsionTorsionParameters() : AmoebaTorsionTorsionForce
• setUnitCellDimensions() : Topology
• setUseDispersionCorrection() : NonbondedForce , AmoebaVdwForce
• setVelocities() : RPMDIntegrator , Context
• setVelocitiesToTemperature() : Context
• setVirtualSite() : System
• step() : CustomIntegrator , VariableLangevinIntegrator , RPMDIntegrator , VerletIntegrator , LangevinIntegrator , VariableVerletIntegrator , BrownianIntegrator , Simulation , Integrator
• stepTo() : VariableVerletIntegrator , VariableLangevinIntegrator
• supportsDoublePrecision() : Platform
• supportsKernels() : Platform