openmmtools.testsystems.TolueneVacuum

class openmmtools.testsystems.TolueneVacuum(constraints=HBonds, hydrogenMass=None, **kwargs)

Toluene GAFF/AM1-BCC in vacuum.

Parameters:

constraintsoptional, default=openmm.app.HBonds

hydrogenMassunit, optional, default=None

If set, will pass along a modified hydrogen mass for OpenMM to use mass repartitioning.

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.

Examples

Create toluene with constraints on bonds to hydrogen >>> testsystem = TolueneVacuum() >>> [system, positions, topology] = [testsystem.system, testsystem.positions, testsystem.topology]

__init__(constraints=HBonds, hydrogenMass=None, **kwargs)

Abstract base class for test system.

Parameters:

Methods

__init__([constraints, hydrogenMass])	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.