Uses of Class
ffx.algorithms.dynamics.MolecularDynamics

Packages that use MolecularDynamics

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
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 MolecularDynamics in ffx.algorithms.cli

Methods in ffx.algorithms.cli that return MolecularDynamics

Modifier and Type	Method	Description
MolecularDynamics	OSTOptions.assembleMolecularDynamics(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, AlgorithmListener algorithmListener)	Assembles a MolecularDynamics wrapped around a Potential.
MolecularDynamics	DynamicsOptions.getDynamics(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener)	Initialize a MolecularDynamics from the parsed options.
MolecularDynamics	DynamicsOptions.getDynamics(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener, MDEngine requestedEngine)	Initialize a MolecularDynamics from the parsed options.
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.

Uses of MolecularDynamics in ffx.algorithms.dynamics

Subclasses of MolecularDynamics in ffx.algorithms.dynamics

Modifier and Type	Class	Description
class	MolecularDynamicsOpenMM	Runs Molecular Dynamics using OpenMM implementation

Methods in ffx.algorithms.dynamics that return MolecularDynamics

Modifier and Type	Method	Description
static MolecularDynamics	MolecularDynamics.dynamicsFactory(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator)	Method that determines whether a dynamics is done by the java implementation native to ffx or the OpenMM implementation
static MolecularDynamics	MolecularDynamics.dynamicsFactory(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator, MDEngine engine)	dynamicsFactory.

Constructors in ffx.algorithms.dynamics with parameters of type MolecularDynamics

Modifier	Constructor	Description
	PhReplicaExchange(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, double[] x, int worldSize)	pHReplicaExchange constructor.
	PhReplicaExchange(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, double[] x, MolecularDynamicsOpenMM molecularDynamicsOpenMM, Potential potential, int worldSize)	OpenMM cycled pHReplicaExchange constructor.
	ReplicaExchange(MolecularDynamics molecularDynamics, AlgorithmListener listener, double temperature, double exponent, boolean monteCarlo)	ReplicaExchange constructor.
	WeightedEnsembleManager(WeightedEnsembleManager.OneDimMetric metric, int optNumPerBin, MolecularDynamics md, File refStructureFile, boolean resample)

Uses of MolecularDynamics in ffx.algorithms.mc

Methods in ffx.algorithms.mc that return MolecularDynamics

Modifier and Type	Method	Description
MolecularDynamics	MDMove.getMD()

Uses of MolecularDynamics in ffx.algorithms.thermodynamics

Methods in ffx.algorithms.thermodynamics that return MolecularDynamics

Modifier and Type	Method	Description
MolecularDynamics	MonteCarloOST.getMD()

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

Modifier and Type	Method	Description
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.