openmmtools.testsystems.AlchemicalWaterBox¶

class openmmtools.testsystems.AlchemicalWaterBox(*args, **kwargs)[source]¶

Water box test system where a single water molecule can be alchemically modified.

Attributes:

analytical_properties: A list of available analytical properties, accessible via ‘get_propertyname(thermodynamic_state)’ calls.
mdtraj_topology: The mdtraj.Topology object corresponding to the test system (read-only).
name: The name of the test system.
positions: The openmm.unit.Quantity object containing the particle positions, with units compatible with openmm.unit.nanometers.
system: The openmm.System object corresponding to the test system.
topology: The openmm.app.Topology object corresponding to the test system.

Methods

`reduced_potential_expectation`(...)	Calculate the expected potential energy in state_sampled_from, divided by kB * T in state_evaluated_in.
`serialize`()	Return the System and positions in serialized XML form.

__init__(*args, **kwargs)[source]¶

Create a water box test system where a single water molecule can be alchemical discharged.

Parameters are inherited from WaterBox.

Examples

Create a waterbox.

>>> waterbox = AlchemicalWaterBox()
>>> [system, positions] = [waterbox.system, waterbox.positions]

Methods

`__init__`(args, *kwargs)	Create a water box test system where a single water molecule can be alchemical discharged.
`reduced_potential_expectation`(...)	Calculate the expected potential energy in state_sampled_from, divided by kB * T in state_evaluated_in.
`serialize`()	Return the System and positions in serialized XML form.

Attributes

`analytical_properties`	A list of available analytical properties, accessible via 'get_propertyname(thermodynamic_state)' calls.
`mdtraj_topology`	The mdtraj.Topology object corresponding to the test system (read-only).
`name`	The name of the test system.
`positions`	The openmm.unit.Quantity object containing the particle positions, with units compatible with openmm.unit.nanometers.
`system`	The openmm.System object corresponding to the test system.
`topology`	The openmm.app.Topology object corresponding to the test system.

openmmtools