openmmtools.testsystems.PowerOscillator¶

class openmmtools.testsystems.PowerOscillator(K=100.0, b=2.0, mass=Quantity(value=39.948, unit=dalton), **kwargs)[source]¶

Create a 3D Power oscillator, with a single particle confined in an isotropic x^b well.

Parameters:

Kopenmm.unit.Quantity, optional, default=100.0: harmonic restraining potential. The units depend on the power, so we accept unitless inputs and add units of the form unit.kilocalories_per_mole / unit.angstrom ** b
massopenmm.unit.Quantity, optional, default=39.948 * unit.amu: particle mass

Notes

Here we assume a potential energy of the form U(x) = k * x^b.

By the generalized equipartition theorem, the expectation of the potential energy is 3 kT / b.

Attributes:

systemopenmm.System: The openmm.System object corresponding to the test system.
positionslist: The openmm.unit.Quantity object containing the particle positions, with units compatible with openmm.unit.nanometers.

Methods

`get_potential_expectation`(state)	Return the expectation of the potential energy, computed analytically or numerically.
`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.

reduced_potential

__init__(K=100.0, b=2.0, mass=Quantity(value=39.948, unit=dalton), **kwargs)[source]¶

Abstract base class for test system.

Methods

`__init__`([K, b, mass])	Abstract base class for test system.
`get_potential_expectation`(state)	Return the expectation of the potential energy, computed analytically or numerically.
`reduced_potential`(beta, a, b, a2, b2)
`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.

openmmtools