Uses of Class
ffx.potential.cli.WriteoutOptions

Packages that use WriteoutOptions

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.

Uses of WriteoutOptions in ffx.algorithms.cli

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

Modifier and Type	Method	Description
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.
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.