openmmtools.testsystems.FlexiblePMEWaterBox¶
- class openmmtools.testsystems.FlexiblePMEWaterBox(*args, **kwargs)[source]¶
Flexible water box using PME electrostatics and tight PME error tolerance.
- 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 flexible water box using PME electrostatics and tight PME error tolerance.
Parameters are inherited from WaterBox (except for constrained or nonbondedMethod).
Examples
Create a default flexible waterbox.
>>> waterbox = FlexiblePMEWaterBox() >>> [system, positions] = [waterbox.system, waterbox.positions]
Methods
__init__
(*args, **kwargs)Create a flexible water box using PME electrostatics and tight PME error tolerance.
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.