openmmtools.testsystems.ConstraintCoupledHarmonicOscillator

class openmmtools.testsystems.ConstraintCoupledHarmonicOscillator(K=Quantity(value=1.0, unit=kilojoule/(nanometer**2*mole)), d=Quantity(value=1.0, unit=nanometer), mass=Quantity(value=39.948, unit=dalton), **kwargs)[source]

Create a pair of particles in 3D harmonic oscillator wells, coupled by a constraint.

Parameters:
K : simtk.unit.Quantity, optional, default=1.0 * unit.kilojoules_per_mole / unit.nanometer**2

harmonic restraining potential

d : simtk.unit.Quantity, optional, default=1.0 * unit.nanometer

distance between harmonic oscillators. Default is Amber GAFF c-c bond.

mass : simtk.unit.Quantity, default=39.948 * unit.amu

particle mass

Notes

The natural period of a harmonic oscillator is T = sqrt(m/K), so you will want to use an integration timestep smaller than ~ T/10.

Examples

Create a constraint-coupled harmonic oscillator with specified mass, distance, and spring constant.

>>> ccho = ConstraintCoupledHarmonicOscillator()
>>> mass = 12.0 * unit.amu
>>> d = 5.0 * unit.angstroms
>>> K = 1.0 * unit.kilocalories_per_mole / unit.angstroms**2
>>> ccho = ConstraintCoupledHarmonicOscillator(K=K, d=d, mass=mass)
>>> system, positions = ccho.system, ccho.positions
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

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__(K=Quantity(value=1.0, unit=kilojoule/(nanometer**2*mole)), d=Quantity(value=1.0, unit=nanometer), mass=Quantity(value=39.948, unit=dalton), **kwargs)[source]

Abstract base class for test system.

Methods

__init__([K, unit, d, unit, mass, unit]) 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 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.

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.