openmmtools.testsystems.LennardJonesGrid¶
- class openmmtools.testsystems.LennardJonesGrid(nx=8, ny=8, nz=8, *args, **kwargs)[source]¶
Create a periodic fluid of Lennard-Jones particles on a grid. Initial positions are assigned using a subrandom grid to minimize steric interactions.
- Parameters:
- nx, ny, nzint, optional, default=8
Number of particles in x, y, and z dimensions.
- reduced_densityfloat, optional, default=0.86
Reduced density (density * sigma**3); default is appropriate for liquid argon.
- massopenmm.unit.Quantity, optional, default=39.9 * unit.amu
mass of each particle; default is appropriate for argon
- sigmaopenmm.unit.Quantity, optional, default=3.4 * unit.angstrom
Lennard-Jones sigma parameter; default is appropriate for argon
- epsilonopenmm.unit.Quantity, optional, default=0.238 * unit.kilocalories_per_mole
Lennard-Jones well depth; default is appropriate for argon
- cutoffopenmm.unit.Quantity, optional, default=None
Cutoff for nonbonded interactions. If None, defaults to 2.5 * sigma
- switch_widthopenmm.unit.Quantity with units compatible with angstroms, optional, default=0.2*unit.angstroms
switching function is turned on at cutoff - switch_width If None, no switch will be applied (e.g. hard cutoff).
- dispersion_correctionbool, optional, default=True
if True, will use analytical dispersion correction (if not using switching function)
Examples
Create default-size Lennard-Jones fluid with initial positions on a grid.
>>> fluid = LennardJonesGrid() >>> system, positions = fluid.system, fluid.positions
Create a box of Lennard-Jones particles with unequal grid spacing.
>>> fluid = LennardJonesGrid(nx=8, ny=9, nz=10) >>> system, positions = fluid.system, fluid.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 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__(nx=8, ny=8, nz=8, *args, **kwargs)[source]¶
Abstract base class for test system.
- Parameters:
Methods
__init__
([nx, ny, nz])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.