openmmtools.testsystems.LysozymeImplicit

class openmmtools.testsystems.LysozymeImplicit(**kwargs)

T4 lysozyme L99A (AMBER ff96) with p-xylene ligand (GAFF + AM1-BCC) in implicit OBC GBSA solvent.

Parameters:

constraintsopenmm.app constraints (None, HBonds, HAngles, AllBonds)

constraints to be imposed

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 T4 lysozyme L99A with p-xylene ligand using OBC1 GBSA. >>> lysozyme = LysozymeImplicit() >>> (system, positions) = lysozyme.system, lysozyme.positions

Create T4 lysozyme L99A with p-xylene ligand using OBC2 GBSA. >>> lysozyme = LysozymeImplicit(implicitSolvent=app.OBC2)

__init__(**kwargs)

Abstract base class for test system.

Parameters:

Methods

__init__(**kwargs)	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.