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)

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)

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.