openmmtools.testsystems.DHFRExplicit¶
- class openmmtools.testsystems.DHFRExplicit(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]¶
Joint Amber CHARMM (JAC) DHFR / TIP3P benchmark system with 23558 atoms.
- Parameters:
- constraintsoptional, default=openmm.app.HBonds
- rigid_waterbool, optional, default=True
- nonbondedCutoffQuantity, optional, default=DEFAULT_CUTOFF_DISTANCE
- use_dispersion_correctionbool, optional, default=True
If True, the long-range disperson correction will be used.
- nonbondedMethodopenmm.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).
- hydrogenMassunit, optional, default=None
If set, will pass along a modified hydrogen mass for OpenMM to use mass repartitioning.
- switch_widthopenmm.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).
- ewaldErrorTolerancefloat, optional, default=DEFAULT_EWALD_ERROR_TOLERANCE
The Ewald or PME tolerance.
Notes
If you are using this testsystem for performance benchmarking, you may wish to tune the nonbondedCutoff to a distance that is optimal for your compute hardware. For modern GPUs, 0.95 nm may be a good place to start.
- 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, 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.
- Parameters:
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 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.