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.