Uses of Class
ffx.potential.SystemState

Packages that use SystemState

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.integrators	The Integrators package implements integrators for molecular dynamics simulations.
ffx.algorithms.dynamics.thermostats	The Thermostats package implements thermostats for molecular dynamics simulations.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.extended	The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e. lambda dynamics on protonation).

Uses of SystemState in ffx.algorithms.dynamics

Fields in ffx.algorithms.dynamics declared as SystemState

Modifier and Type	Field	Description
protected final SystemState	MolecularDynamics.state	Stores the current molecular dynamics state.

Uses of SystemState in ffx.algorithms.dynamics.integrators

Fields in ffx.algorithms.dynamics.integrators declared as SystemState

Modifier and Type	Field	Description
protected final SystemState	Integrator.state	The MDState class contains the current state of the Molecular Dynamics simulation.

Constructors in ffx.algorithms.dynamics.integrators with parameters of type SystemState

Modifier	Constructor	Description
	BetterBeeman(SystemState state)	Constructor for BetterBeeman.
	Integrator(SystemState state)	Constructor for Integrator.
	Respa(SystemState state)	Initialize Respa multiple time step molecular dynamics.
	Stochastic(double friction, SystemState state)	Constructor for Stochastic Dynamics.
	VelocityVerlet(SystemState state)	Constructor for VelocityVerlet.

Uses of SystemState in ffx.algorithms.dynamics.thermostats

Fields in ffx.algorithms.dynamics.thermostats declared as SystemState

Modifier and Type	Field	Description
protected final SystemState	Thermostat.state	The molecular dynamics state to be used.

Constructors in ffx.algorithms.dynamics.thermostats with parameters of type SystemState

Modifier	Constructor	Description
	Adiabatic(SystemState state, Potential.VARIABLE_TYPE[] type)	Constructor for Adiabatic.
	Adiabatic(SystemState state, Potential.VARIABLE_TYPE[] type, List<Constraint> constraints)
	Berendsen(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature)	Constructor for Berendsen.
	Berendsen(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature, double tau)	Constructor for Berendsen.
	Berendsen(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature, double tau, List<Constraint> constraints)
	Bussi(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature)	Constructor for Bussi.
	Bussi(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature, double tau)	Constructor for Bussi.
	Bussi(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature, double tau, List<Constraint> constraints)
	Thermostat(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature)	Constructor for Thermostat.
	Thermostat(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature, List<Constraint> constraints)

Uses of SystemState in ffx.potential

Constructors in ffx.potential with parameters of type SystemState

Modifier	Constructor	Description
	UnmodifiableState(SystemState state)	This constructor does a defensive copy of all arrays.

Uses of SystemState in ffx.potential.extended

Methods in ffx.potential.extended that return SystemState

Modifier and Type	Method	Description
SystemState	ExtendedSystem.getState()