openmmtools.testsystems.MolecularIdealGas¶

class openmmtools.testsystems.MolecularIdealGas(shake=None, nonbondedCutoff=7.0 A, nonbondedMethod=CutoffPeriodic, **kwargs)[source]¶

Molecular ideal gas (methanol box).

Parameters:

shakestring, optional, default=None
nonbondedCutoffQuantity, optional, default=7.0 * unit.angstroms
nonbondedMethodopenmm.app nonbonded method, optional, default=app.PME: Sets the nonbonded method to use for the water box (one of app.CutoffPeriodic, app.Ewald, app.PME).

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.

Examples

>>> methanol_box = MolecularIdealGas()
>>> system, positions = methanol_box.system, methanol_box.positions

__init__(shake=None, nonbondedCutoff=7.0 A, nonbondedMethod=CutoffPeriodic, **kwargs)[source]¶

Abstract base class for test system.

Methods

`__init__`([shake, nonbondedCutoff, ...])	Abstract base class for test system.
`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.

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