openmmtools.testsystems.CustomExternalForcesTestSystem

class openmmtools.testsystems.CustomExternalForcesTestSystem(energy_expressions=('x^2 + y^2 + z^2', ), mass=Quantity(value=39.948, unit=dalton), n_particles=500, **kwargs)[source]

Create a system with an arbitrary number of CustomExternalForces.

Parameters:
energy_expressions : tuple(string)

Each string in the tuple will add a CustomExternalForce to the OpenMM system. Each force will be assigned a different force group, starting with 0. By default this will be a 3D harmonic oscillator.

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

particle mass. Default corresponds to argon.

n_particles : int, optional, default=500

Number of (identical) particles to add.

Notes

This may be useful for testing multiple timestep integrators.

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

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__(energy_expressions=('x^2 + y^2 + z^2', ), mass=Quantity(value=39.948, unit=dalton), n_particles=500, **kwargs)[source]

Abstract base class for test system.

Methods

__init__([energy_expressions, 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.