- s -

• saveCheckpoint() : Simulation
• saveState() : Simulation
• 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() : CustomBondForce , CustomCentroidBondForce , CustomCompoundBondForce , HarmonicBondForce , AmoebaBondForce
• setBox() : CharmmPsfFile
• setComputedValueParameters() : CustomGBForce
• setConstraintParameters() : System
• setConstraintTolerance() : Integrator , CompoundIntegrator
• setCovalentMap() : AmoebaMultipoleForce
• setCurrentIntegrator() : CompoundIntegrator
• setCutoff() : AmoebaVdwForce
• setCutoffDistance() : AmoebaMultipoleForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , GBSAOBCForce , 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 , CustomCentroidBondForce , 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 , CustomCentroidBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , CustomTorsionForce
• setGlobalParameterName() : CustomNonbondedForce , CustomTorsionForce , CustomAngleForce , CustomBondForce , CustomCentroidBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce
• setGlobalVariable() : CustomIntegrator
• setGlobalVariableByName() : CustomIntegrator
• setGroupParameters() : CustomCentroidBondForce
• setIncludeCavityTerm() : AmoebaGeneralizedKirkwoodForce
• setInteractionGroupParameters() : CustomNonbondedForce
• setKineticEnergyExpression() : CustomIntegrator
• setMapParameters() : CMAPTorsionForce
• setMaxDrudeDistance() : DrudeLangevinIntegrator
• setMinimizationErrorTolerance() : DrudeSCFIntegrator
• setMultipoleParameters() : AmoebaMultipoleForce
• setMutualInducedMaxIterations() : AmoebaMultipoleForce
• setMutualInducedTargetEpsilon() : AmoebaMultipoleForce
• setNonbondedMethod() : AmoebaMultipoleForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , GBSAOBCForce , NonbondedForce , AmoebaVdwForce
• setOutOfPlaneBendParameters() : AmoebaOutOfPlaneBendForce
• setParameter() : Context
• setParticleExclusions() : AmoebaVdwForce
• setParticleMass() : System
• setParticleParameters() : AmoebaGeneralizedKirkwoodForce , AmoebaWcaDispersionForce , CustomExternalForce , CustomGBForce , CustomNonbondedForce , DrudeForce , GBSAOBCForce , NonbondedForce , CustomManyParticleForce , AmoebaVdwForce
• setPerAcceptorParameterName() : CustomHbondForce
• setPerAngleParameterName() : CustomAngleForce
• setPerBondParameterName() : CustomBondForce , CustomCompoundBondForce , CustomCentroidBondForce
• setPerDofVariable() : CustomIntegrator
• setPerDofVariableByName() : CustomIntegrator
• setPerDonorParameterName() : CustomHbondForce
• setPeriodicBoxVectors() : Context , Topology
• setPermutationMode() : CustomManyParticleForce
• setPerParticleParameterName() : CustomExternalForce , CustomGBForce , CustomManyParticleForce , CustomNonbondedForce
• setPerTorsionParameterName() : CustomTorsionForce
• setPiTorsionParameters() : AmoebaPiTorsionForce
• setPmeGridDimensions() : AmoebaMultipoleForce
• setPMEParameters() : NonbondedForce
• setPolarizationType() : AmoebaMultipoleForce
• setPositions() : RPMDIntegrator , Context
• setProbeRadius() : AmoebaGeneralizedKirkwoodForce
• setPropertyDefaultValue() : Platform
• setPropertyValue() : Platform
• setRandomNumberSeed() : BrownianIntegrator , VariableLangevinIntegrator , CustomIntegrator , MonteCarloBarostat , RPMDIntegrator , RPMDMonteCarloBarostat , DrudeLangevinIntegrator , LangevinIntegrator , MonteCarloAnisotropicBarostat , MonteCarloMembraneBarostat , AndersenThermostat
• setReactionFieldDielectric() : NonbondedForce
• setReciprocalSpaceForceGroup() : NonbondedForce
• setRminh() : AmoebaWcaDispersionForce
• setRmino() : AmoebaWcaDispersionForce
• setScreenedPairParameters() : DrudeForce
• setShctd() : AmoebaWcaDispersionForce
• setSigmaCombiningRule() : AmoebaVdwForce
• setSlevy() : AmoebaWcaDispersionForce
• setSoluteDielectric() : AmoebaGeneralizedKirkwoodForce , GBSAOBCForce
• setSolventDielectric() : AmoebaGeneralizedKirkwoodForce , GBSAOBCForce
• setState() : Context
• setStepSize() : Integrator , CompoundIntegrator
• setStretchBendParameters() : AmoebaStretchBendForce
• setSurfaceAreaEnergy() : GBSAOBCForce
• setSurfaceAreaFactor() : AmoebaGeneralizedKirkwoodForce
• setSwitchingDistance() : CustomNonbondedForce , NonbondedForce
• setTemperature() : DrudeLangevinIntegrator , RPMDIntegrator , LangevinIntegrator , MonteCarloMembraneBarostat , VariableLangevinIntegrator , MonteCarloAnisotropicBarostat , MonteCarloBarostat , BrownianIntegrator
• setTime() : Context
• setTorsionParameters() : CMAPTorsionForce , CustomTorsionForce , PeriodicTorsionForce , RBTorsionForce
• setTorsionTorsionGrid() : AmoebaTorsionTorsionForce
• setTorsionTorsionParameters() : AmoebaTorsionTorsionForce
• setTypeFilter() : CustomManyParticleForce
• setUnitCellDimensions() : Topology
• setUseDispersionCorrection() : AmoebaVdwForce , NonbondedForce
• setUseLongRangeCorrection() : CustomNonbondedForce
• setUseSwitchingFunction() : CustomNonbondedForce , NonbondedForce
• setVelocities() : RPMDIntegrator , Context
• setVelocitiesToTemperature() : Context
• setVirtualSite() : System
• setXYMode() : MonteCarloMembraneBarostat
• setZMode() : MonteCarloMembraneBarostat
• step() : Simulation , CompoundIntegrator , VariableLangevinIntegrator , DrudeLangevinIntegrator , CustomIntegrator , LangevinIntegrator , DrudeSCFIntegrator , VariableVerletIntegrator , RPMDIntegrator , Integrator , VerletIntegrator , BrownianIntegrator
• stepTo() : VariableVerletIntegrator , VariableLangevinIntegrator
• supportsDoublePrecision() : Platform
• supportsKernels() : Platform
• SurfaceTension() : MonteCarloMembraneBarostat
• symbol() : Element
• system() : CharmmPsfFile