openmmtools.testsystems.WaterCluster

class openmmtools.testsystems.WaterCluster(n_waters=20, K=Quantity(value=1.0, unit=kilojoule / nanometer**2 * mole), model='tip3p', constrained=True, restrain_only_oxygen=False, **kwargs)

Create a few water molecules in a harmonic restraining potential

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.

__init__(n_waters=20, K=Quantity(value=1.0, unit=kilojoule / nanometer**2 * mole), model='tip3p', constrained=True, restrain_only_oxygen=False, **kwargs)

Parameters:

n_watersint

Number of water molecules in the cluster

Kopenmm.unit.Quantity (energy / distance^2)

spring constant for restraining potential

modelstring

Must be one of [‘tip3p’, ‘tip4pew’, ‘tip5p’, ‘spce’]

constrained: bool

Whether to use rigid water or not

restrain_only_oxygen: bool

Whether to apply the restraining potential to oxygens only (True) or to all atoms (False)

Examples

Create water cluster with default settings

>>> cluster = WaterCluster()
>>> system, positions = cluster.system, cluster.positions

Methods

__init__([n_waters, K, model, constrained, ...])
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.