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)

Create a pair of Lennard-Jones particles.

Parameters:

massopenmm.unit.Quantity with units compatible with amu, optional, default=39.9*amu

The mass of each particle.

epsilonopenmm.unit.Quantity with units compatible with kilojoules_per_mole, optional, default=1.0*kilocalories_per_mole

The effective Lennard-Jones sigma parameter.

sigmaopenmm.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 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

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)

Abstract base class for test system.

Parameters:

Methods

__init__([mass, sigma, 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 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.