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.