Uses of Class
ffx.algorithms.cli.DynamicsOptions

Packages that use DynamicsOptions

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.mc	The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.algorithms.thermodynamics	The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).

Uses of DynamicsOptions in ffx.algorithms.cli

Methods in ffx.algorithms.cli with parameters of type DynamicsOptions

Modifier and Type	Method	Description
CrystalPotential	OSTOptions.applyAllOSTOptions(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly firstAssembly, DynamicsOptions dynamicsOptions, BarostatOptions barostatOptions)	Applies relevant options to an OST, and returns either the OST object or something that wraps the OST (such as a Barostat).
MolecularDynamics	OSTOptions.assembleMolecularDynamics(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, AlgorithmListener algorithmListener)	Assembles a MolecularDynamics wrapped around a Potential.
void	OSTOptions.beginMCOST(MonteCarloOST monteCarloOST, DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions)	Runs MC-OST.
void	OSTOptions.beginMDOST(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, ThermodynamicsOptions thermodynamicsOptions, File dynFile, AlgorithmListener algorithmListener)	Begins MD-OST sampling from an assembled OST.
OrthogonalSpaceTempering	OSTOptions.constructOST(CrystalPotential crystalPotential, File lambdaRestartFile, File histogramRestartFile, MolecularAssembly firstAssembly, org.apache.commons.configuration2.Configuration addedProperties, DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions, LambdaParticleOptions lambdaParticleOptions, AlgorithmListener algorithmListener, boolean async)	constructOST.
SimulatedAnnealing	AnnealOptions.createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener)	Creates a SimulatedAnnealing object.
SimulatedAnnealing	AnnealOptions.createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, File dynFile)	Creates a SimulatedAnnealing object.
MolecularDynamics	ThermodynamicsOptions.runFixedAlchemy(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener)	Run an alchemical free energy window.
MolecularDynamics	ThermodynamicsOptions.runNEQ(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener)	Run a non-equilibrium alchemical free energy simulation.
MonteCarloOST	OSTOptions.setupMCOST(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly[] molecularAssemblies, DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions, boolean verbose, File dynRestart, AlgorithmListener algorithmListener)	setupMCOST.

Uses of DynamicsOptions in ffx.algorithms.mc

Constructors in ffx.algorithms.mc with parameters of type DynamicsOptions

Modifier	Constructor	Description
	MDMove(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, DynamicsOptions dynamics, long stepsPerCycle, File dynRestartFile)	Constructor for MDMove.

Uses of DynamicsOptions in ffx.algorithms.thermodynamics

Methods in ffx.algorithms.thermodynamics with parameters of type DynamicsOptions

Modifier and Type	Method	Description
static RepExOST	RepExOST.repexMC(OrthogonalSpaceTempering orthogonalSpaceTempering, MonteCarloOST monteCarloOST, DynamicsOptions dynamicsOptions, OSTOptions ostOptions, org.apache.commons.configuration2.CompositeConfiguration compositeConfiguration, String fileType, boolean twoStep, double repexInterval)	Construct a RepExOST for Monte Carlo orthogonal space tempering.
static RepExOST	RepExOST.repexMD(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularDynamics molecularDynamics, DynamicsOptions dynamicsOptions, OSTOptions ostOptions, org.apache.commons.configuration2.CompositeConfiguration compositeConfiguration, String fileType, double repexInterval)	Construct a RepExOST for Molecular Dynamics orthogonal space tempering.

Constructors in ffx.algorithms.thermodynamics with parameters of type DynamicsOptions

Modifier	Constructor	Description
	MonteCarloOST(Potential potentialEnergy, OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly molecularAssembly, org.apache.commons.configuration2.CompositeConfiguration properties, AlgorithmListener listener, DynamicsOptions dynamics, boolean verbose, int cycleLength, File dynRestartFile)	Constructor for MonteCarloOST.
	OrthogonalSpaceTempering(LambdaInterface lambdaInterface, CrystalPotential potential, HistogramData histogramData, LambdaData lambdaData, org.apache.commons.configuration2.CompositeConfiguration properties, DynamicsOptions dynamicsOptions, LambdaParticleOptions lambdaParticleOptions, AlgorithmListener algorithmListener)	OST Constructor.