openmmtools.testsystems.AlanineDipeptideExplicit

class openmmtools.testsystems.AlanineDipeptideExplicit(constraints=HBonds, rigid_water=True, nonbondedCutoff=Quantity(value=10.0, unit=angstrom), use_dispersion_correction=True, nonbondedMethod=PME, hydrogenMass=None, switch_width=Quantity(value=1.5, unit=angstrom), ewaldErrorTolerance=1e-05, **kwargs)[source]

Alanine dipeptide ff96 in TIP3P explicit solvent..

Parameters:
constraints : optional, default=simtk.openmm.app.HBonds
rigid_water : bool, optional, default=True
nonbondedCutoff : Quantity, optional, default=9.0 * unit.angstroms
use_dispersion_correction : bool, optional, default=True

If True, the long-range disperson correction will be used.

nonbondedMethod : simtk.openmm.app nonbonded method, optional, default=app.PME

Sets the nonbonded method to use for the water box (one of app.CutoffPeriodic, app.Ewald, app.PME).

hydrogenMass : unit, optional, default=None

If set, will pass along a modified hydrogen mass for OpenMM to use mass repartitioning.

cutoff : simtk.unit.Quantity with units compatible with angstroms, optional, default = DEFAULT_CUTOFF_DISTANCE

Cutoff distance

switch_width : simtk.unit.Quantity with units compatible with angstroms, optional, default = DEFAULT_SWITCH_WIDTH

switching function is turned on at cutoff - switch_width If None, no switch will be applied (e.g. hard cutoff).

ewaldErrorTolerance : float, optional, default=DEFAULT_EWALD_ERROR_TOLERANCE

The Ewald or PME tolerance.

Examples

>>> alanine = AlanineDipeptideExplicit()
>>> (system, positions) = alanine.system, alanine.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

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__(constraints=HBonds, rigid_water=True, nonbondedCutoff=Quantity(value=10.0, unit=angstrom), use_dispersion_correction=True, nonbondedMethod=PME, hydrogenMass=None, switch_width=Quantity(value=1.5, unit=angstrom), ewaldErrorTolerance=1e-05, **kwargs)[source]

Abstract base class for test system.

Methods

__init__([constraints, rigid_water, …]) 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 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.

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.