Uses of Class
ffx.algorithms.dynamics.thermostats.Thermostat

Packages that use Thermostat

Package	Description
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.dynamics.thermostats	The Thermostats package implements thermostats for molecular dynamics simulations.
ffx.algorithms.mc	The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.

Uses of Thermostat in ffx.algorithms.dynamics

Methods in ffx.algorithms.dynamics that return Thermostat

Modifier and Type	Method	Description
Thermostat	MolecularDynamics.getThermostat()	Getter for the field thermostat.

Methods in ffx.algorithms.dynamics with parameters of type Thermostat

Modifier and Type	Method	Description
void	MolecularDynamics.setThermostat(Thermostat thermostat)	Setter for the field thermostat.

Uses of Thermostat in ffx.algorithms.dynamics.thermostats

Subclasses of Thermostat in ffx.algorithms.dynamics.thermostats

Modifier and Type	Class	Description
class	Adiabatic	The Adiabatic thermostat is for NVE simulations and does not alter particle velocities.
class	Berendsen	Thermostat a molecular dynamics trajectory to an external bath using the Berendsen weak-coupling thermostat.
class	Bussi	Thermostat a molecular dynamics trajectory to an external bath using the Bussi, Donadio, and Parrinello method.

Uses of Thermostat in ffx.algorithms.mc

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

Modifier	Constructor	Description
	RosenbluthCBMC(MolecularAssembly molecularAssembly, ForceFieldEnergy ffe, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize, boolean writeSnapshots)	RRMC constructor.
	RosenbluthOBMC(MolecularAssembly molecularAssembly, ForceFieldEnergy forceFieldEnergy, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize)	RRMC constructor.
	RosenbluthOBMC(MolecularAssembly molecularAssembly, ForceFieldEnergy forceFieldEnergy, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize, boolean writeSnapshots)	Constructor for RosenbluthOBMC.

Uses of Thermostat in ffx.xray

Fields in ffx.xray declared as Thermostat

Modifier and Type	Field	Description
protected Thermostat	RefinementEnergy.thermostat	A thermostat instance.

Methods in ffx.xray that return Thermostat

Modifier and Type	Method	Description
Thermostat	RefinementEnergy.getThermostat()	Getter for the field thermostat.

Methods in ffx.xray with parameters of type Thermostat

Modifier and Type	Method	Description
void	RefinementEnergy.setThermostat(Thermostat thermostat)	Setter for the field thermostat.