openmmtools.testsystems.LennardJonesPair

class openmmtools.testsystems.LennardJonesPair(mass=Quantity(value=39.9, unit=dalton), sigma=Quantity(value=3.35, unit=angstrom), epsilon=Quantity(value=10.0, unit=kilocalorie/mole), **kwargs)[source]

Create a pair of Lennard-Jones particles.

Parameters:
mass : simtk.unit.Quantity with units compatible with amu, optional, default=39.9*amu

The mass of each particle.

epsilon : simtk.unit.Quantity with units compatible with kilojoules_per_mole, optional, default=1.0*kilocalories_per_mole

The effective Lennard-Jones sigma parameter.

sigma : simtk.unit.Quantity with units compatible with nanometers, optional, default=3.350*angstroms

The effective Lennard-Jones sigma parameter.

Examples

Create Lennard-Jones pair.

>>> test = LennardJonesPair()
>>> system, positions = test.system, test.positions
>>> thermodynamic_state = ThermodynamicState(temperature=300.0*unit.kelvin)
>>> binding_free_energy = test.get_binding_free_energy(thermodynamic_state)

Create Lennard-Jones pair with different well depth.

>>> test = LennardJonesPair(epsilon=11.0*unit.kilocalories_per_mole)
>>> system, positions = test.system, test.positions
>>> thermodynamic_state = ThermodynamicState(temperature=300.0*unit.kelvin)
>>> binding_free_energy = test.get_binding_free_energy(thermodynamic_state)

Create Lennard-Jones pair with different well depth and sigma.

>>> test = LennardJonesPair(epsilon=7.0*unit.kilocalories_per_mole, sigma=4.5*unit.angstroms)
>>> system, positions = test.system, test.positions
>>> thermodynamic_state = ThermodynamicState(temperature=300.0*unit.kelvin)
>>> binding_free_energy = test.get_binding_free_energy(thermodynamic_state)
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.

Methods

get_binding_free_energy(thermodynamic_state) Compute the binding free energy of the two particles at the given thermodynamic state.
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__(mass=Quantity(value=39.9, unit=dalton), sigma=Quantity(value=3.35, unit=angstrom), epsilon=Quantity(value=10.0, unit=kilocalorie/mole), **kwargs)[source]

Abstract base class for test system.

Methods

__init__([mass, unit, sigma, unit, epsilon, …]) Abstract base class for test system.
get_binding_free_energy(thermodynamic_state) Compute the binding free energy of the two particles at the given thermodynamic state.
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_binding_free_energy(thermodynamic_state)[source]

Compute the binding free energy of the two particles at the given thermodynamic state.

Parameters:
thermodynamic_state : ThermodynamicState

The thermodynamic state specifying the temperature for which the binding free energy is to be computed.

This is currently computed by numerical integration.
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.