openmmtools.testsystems.PowerOscillator

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

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

Parameters:

K : simtk.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

mass : simtk.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:

system : simtk.openmm.System

The simtk.openmm.System object corresponding to the test system.

positions : list

The simtk.unit.Quantity object containing the particle positions, with units compatible with simtk.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)

Abstract base class for test system.

Methods

__init__([K, b, mass, unit])	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 simtk.unit.Quantity object containing the particle positions, with units compatible with simtk.unit.nanometers.
system	The simtk.openmm.System object corresponding to the test system.
topology	The simtk.openmm.app.Topology object corresponding to the test system.

analytical_properties

A list of available analytical properties, accessible via ‘get_propertyname(thermodynamic_state)’ calls.

get_potential_expectation(state)

Return the expectation of the potential energy, computed analytically or numerically.

Returns:

potential_mean : simtk.unit.Quantity compatible with simtk.unit.kilojoules_per_mole

The expectation of the potential energy.

mdtraj_topology

The mdtraj.Topology object corresponding to the test system (read-only).

name

The name of the test system.

positions

The simtk.unit.Quantity object containing the particle positions, with units compatible with simtk.unit.nanometers.

reduced_potential_expectation(state_sampled_from, state_evaluated_in)

Calculate the expected potential energy in state_sampled_from, divided by kB * T in state_evaluated_in.

Notes

This is not called get_reduced_potential_expectation because this function requires two, not one, inputs.

serialize()

Return the System and positions in serialized XML form.

Returns:

system_xml : str

Serialized XML form of System object.

state_xml : str

Serialized XML form of State object containing particle positions.

system

The simtk.openmm.System object corresponding to the test system.

topology

The simtk.openmm.app.Topology object corresponding to the test system.