openmmtools.testsystems.GiantFlexibleDischargedWaterBox

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

Flexible water box.

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 large flexible discharged water box (50A x 50A x 50A).

Parameters are inherited from WaterBox (except for ‘constrained’).

Examples

Create a default giant flexible discharged waterbox.

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

Methods

__init__(*args, **kwargs)

Create a large flexible discharged water box (50A x 50A x 50A).

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.