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.