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)

Create a system with an arbitrary number of CustomExternalForces.

Parameters:

energy_expressionstuple(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.

massopenmm.unit.Quantity, optional, default=39.948 * unit.amu

particle mass. Default corresponds to argon.

n_particlesint, optional, default=500

Number of (identical) particles to add.

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

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.

Notes

This may be useful for testing multiple timestep integrators.

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

Abstract base class for test system.

Parameters:

Methods

__init__([energy_expressions, mass, n_particles])	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 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.