openmmtools.testsystems.AlanineDipeptideImplicit

class openmmtools.testsystems.AlanineDipeptideImplicit(constraints=HBonds, hydrogenMass=None, **kwargs)[source]

Alanine dipeptide ff96 in OBC GBSA implicit solvent.

Parameters:
constraintsoptional, default=openmm.app.HBonds
hydrogenMassunit, optional, default=None

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

Examples

Create alanine dipeptide with constraints on bonds to hydrogen >>> alanine = AlanineDipeptideImplicit() >>> (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 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__(constraints=HBonds, hydrogenMass=None, **kwargs)[source]

Abstract base class for test system.

Parameters:

Methods

__init__([constraints, hydrogenMass])

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.