openmmtools.testsystems.Diatom

class openmmtools.testsystems.Diatom(K=Quantity(value=290.1, unit=kilocalorie/(angstrom**2*mole)), r0=Quantity(value=1.55, unit=angstrom), m1=Quantity(value=39.948, unit=dalton), m2=Quantity(value=39.948, unit=dalton), constraint=False, use_central_potential=False, **kwargs)[source]

Create a free diatomic molecule with a single harmonic bond between the two atoms.

Parameters:
K : simtk.unit.Quantity, optional, default=290.1 * unit.kilocalories_per_mole / unit.angstrom**2

harmonic bond potential. default is GAFF c-c bond

r0 : simtk.unit.Quantity, optional, default=1.550 * unit.amu

bond length. Default is Amber GAFF c-c bond.

constraint : bool, default=False

if True, the bond length will be constrained

m1 : simtk.unit.Quantity, optional, default=12.01 * unit.amu

particle1 mass

m2 : simtk.unit.Quantity, optional, default=12.01 * unit.amu

particle2 mass

use_central_potential : bool, optional, default=False

if True, a soft central potential will also be added to keep the system from drifting away

Notes

The natural period of a harmonic oscillator is T = sqrt(m/K), so you will want to use an integration timestep smaller than ~ T/10.

Examples

Create a Diatom:

>>> diatom = Diatom()
>>> system, positions = diatom.system, diatom.positions

Create a Diatom with constraint in a central potential >>> diatom = Diatom(constraint=True, use_central_potential=True) >>> system, positions = diatom.system, diatom.positions

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

get_potential_expectation(state) Return the expectation of the potential energy, computed analytically or numerically.
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__(K=Quantity(value=290.1, unit=kilocalorie/(angstrom**2*mole)), r0=Quantity(value=1.55, unit=angstrom), m1=Quantity(value=39.948, unit=dalton), m2=Quantity(value=39.948, unit=dalton), constraint=False, use_central_potential=False, **kwargs)[source]

Abstract base class for test system.

Methods

__init__([K, unit, r0, unit, m1, unit, m2, …]) Abstract base class for test system.
get_potential_expectation(state) Return the expectation of the potential energy, computed analytically or numerically.
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.

get_potential_expectation(state)[source]

Return the expectation of the potential energy, computed analytically or numerically.

Parameters:
state : ThermodynamicState with temperature defined

The thermodynamic state at which the property is to be computed.
Returns:
potential_mean : simtk.unit.Quantity compatible with simtk.unit.kilojoules_per_mole

The expectation of the potential energy.
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.