openmmtools.testsystems.LennardJonesCluster

class openmmtools.testsystems.LennardJonesCluster(nx=3, ny=3, nz=3, K=1.0 kJ/(nm**2 mol), cutoff=None, switch_width=None, **kwargs)

Create a non-periodic rectilinear grid of Lennard-Jones particles in a harmonic restraining potential.

Parameters:

nxint, optional, default=3

number of particles in the x direction

nyint, optional, default=3

number of particles in the y direction

nzint, optional, default=3

number of particles in the z direction

Kopenmm.unit.Quantity, optional, default=1.0 * unit.kilojoules_per_mole/unit.nanometer**2

harmonic restraining potential

cutoffopenmm.unit.Quantity, optional, default=None

If None, will use NoCutoff for the NonbondedForce. Otherwise, use CutoffNonPeriodic with the specified cutoff.

switch_widthopenmm.unit.Quantity, optional, default=None

If None, the cutoff is a hard cutoff. If switch_width is specified, use a switching function with this width.

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 Lennard-Jones cluster.

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

Create default 3x3x3 Lennard-Jones cluster in a harmonic restraining potential.

>>> cluster = LennardJonesCluster(nx=10, ny=10, nz=10)
>>> system, positions = cluster.system, cluster.positions

__init__(nx=3, ny=3, nz=3, K=1.0 kJ/(nm**2 mol), cutoff=None, switch_width=None, **kwargs)

Abstract base class for test system.

Parameters:

Methods

__init__([nx, ny, nz, K, cutoff, switch_width])	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.