openmmtools.testsystems.IdealGas

class openmmtools.testsystems.IdealGas(nparticles=216, mass=Quantity(value=39.9, unit=dalton), temperature=Quantity(value=298.0, unit=kelvin), pressure=Quantity(value=1.0, unit=atmosphere), volume=None, **kwargs)

Create an ‘ideal gas’ of noninteracting particles in a periodic box.

Parameters:

nparticlesint, optional, default=216

number of particles

massint, optional, default=39.9 * unit.amu

temperatureint, optional, default=298.0 * unit.kelvin

pressureint, optional, default=1.0 * unit.atmosphere

volumeNone

if None, defaults to (nparticles * temperature * unit.BOLTZMANN_CONSTANT_kB / pressure).in_units_of(unit.nanometers**3)

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_kinetic_expectation(state)	Return the expectation of the kinetic energy, computed analytically or numerically.
get_kinetic_standard_deviation(state)	Return the standard deviation of the kinetic energy, computed analytically or numerically.
get_potential_expectation(state)	Return the expectation of the potential energy, computed analytically or numerically.
get_potential_standard_deviation(state)	Return the standard deviation of the potential energy, computed analytically or numerically.
get_volume_expectation(state)	Return the expectation of the volume, computed analytically.
get_volume_standard_deviation(state)	Return the standard deviation of the volume, computed analytically.
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 an ideal gas system.

>>> gas = IdealGas()
>>> system, positions = gas.system, gas.positions

Create a smaller ideal gas system containing 64 particles.

>>> gas = IdealGas(nparticles=64)
>>> system, positions = gas.system, gas.positions

__init__(nparticles=216, mass=Quantity(value=39.9, unit=dalton), temperature=Quantity(value=298.0, unit=kelvin), pressure=Quantity(value=1.0, unit=atmosphere), volume=None, **kwargs)

Abstract base class for test system.

Parameters:

Methods

__init__([nparticles, mass, temperature, ...])	Abstract base class for test system.
get_kinetic_expectation(state)	Return the expectation of the kinetic energy, computed analytically or numerically.
get_kinetic_standard_deviation(state)	Return the standard deviation of the kinetic energy, computed analytically or numerically.
get_potential_expectation(state)	Return the expectation of the potential energy, computed analytically or numerically.
get_potential_standard_deviation(state)	Return the standard deviation of the potential energy, computed analytically or numerically.
get_volume_expectation(state)	Return the expectation of the volume, computed analytically.
get_volume_standard_deviation(state)	Return the standard deviation of the volume, computed analytically.
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.