openmmtools.testsystems.Diatom

class openmmtools.testsystems.Diatom(K=290.1 kcal/(A**2 mol), r0=1.55 A, m1=39.948 Da, m2=39.948 Da, constraint=False, use_central_potential=False, **kwargs)

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

Parameters:

Kopenmm.unit.Quantity, optional, default=290.1 * unit.kilocalories_per_mole / unit.angstrom**2

harmonic bond potential. default is GAFF c-c bond

r0openmm.unit.Quantity, optional, default=1.550 * unit.amu

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

constraintbool, default=False

if True, the bond length will be constrained

m1openmm.unit.Quantity, optional, default=12.01 * unit.amu

particle1 mass

m2openmm.unit.Quantity, optional, default=12.01 * unit.amu

particle2 mass

use_central_potentialbool, optional, default=False

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

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_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.

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

__init__(K=290.1 kcal/(A**2 mol), r0=1.55 A, m1=39.948 Da, m2=39.948 Da, constraint=False, use_central_potential=False, **kwargs)

Abstract base class for test system.

Parameters:

Methods

__init__([K, r0, m1, m2, constraint, ...])	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 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.