Test Systems

openmmtools.testsystems contains a variety of test systems useful for benchmarking, validation, testing, and debugging.

Analytically tractable systems

These test systems are simple test systems where some properties are analytically tractable.

HarmonicOscillator

Create a 3D harmonic oscillator, with a single particle confined in an isotropic harmonic well.

PowerOscillator

Create a 3D Power oscillator, with a single particle confined in an isotropic x^b well.

ConstraintCoupledHarmonicOscillator

Create a pair of particles in 3D harmonic oscillator wells, coupled by a constraint.

HarmonicOscillatorArray

Create a 1D array of noninteracting particles in 3D harmonic oscillator wells.

IdealGas

Create an 'ideal gas' of noninteracting particles in a periodic box.

MolecularIdealGas

Molecular ideal gas (methanol box).

Diatom

Create a free diatomic molecule with a single harmonic bond between the two atoms.

CustomExternalForcesTestSystem

Create a system with an arbitrary number of CustomExternalForces.

CustomGBForceSystem

A system of particles with a CustomGBForce.

LennardJonesPair

Create a pair of Lennard-Jones particles.

Clusters and simple fluids

DiatomicFluid

Create a diatomic fluid.

UnconstrainedDiatomicFluid

Examples

ConstrainedDiatomicFluid

Examples

DipolarFluid

Examples

UnconstrainedDipolarFluid

Examples

ConstrainedDipolarFluid

Examples

LennardJonesCluster

Create a non-periodic rectilinear grid of Lennard-Jones particles in a harmonic restraining potential.

LennardJonesFluid

Create a periodic fluid of Lennard-Jones particles.

LennardJonesFluidTruncated

Lennard-Jones fluid with truncated potential (instead of switched).

LennardJonesFluidSwitched

Lennard-Jones fluid with switched potential (instead of truncated).

LennardJonesGrid

Create a periodic fluid of Lennard-Jones particles on a grid.

CustomLennardJonesFluidMixture

Create a periodic rectilinear grid of Lennard-Jones particles, but implemented via CustomBondForce and NonbondedForce.

WCAFluid

Attributes:

DoubleWellDimer_WCAFluid

Attributes:

DoubleWellChain_WCAFluid

Attributes:

TolueneVacuum

Toluene GAFF/AM1-BCC in vacuum.

TolueneImplicit

Toluene GAFF/AM1-BCC in implicit solvent.

TolueneImplicitHCT

Attributes:

TolueneImplicitOBC1

Attributes:

TolueneImplicitOBC2

Attributes:

TolueneImplicitGBn

Attributes:

TolueneImplicitGBn2

Attributes:

MethanolBox

Methanol box.

WaterCluster

Create a few water molecules in a harmonic restraining potential

Solids

SodiumChlorideCrystal

Create an FCC crystal of sodium chloride.

Water boxes

WaterBox

Create a water box test system.

FlexibleWaterBox

Flexible water box.

FlexibleReactionFieldWaterBox

Flexible water box using reaction field electrostatics.

FlexiblePMEWaterBox

Flexible water box using PME electrostatics and tight PME error tolerance.

PMEWaterBox

Water box using PME electrostatics and tight PME error tolerance.

GiantFlexibleWaterBox

Flexible water box.

FourSiteWaterBox

Four-site water box (TIP4P-Ew).

FiveSiteWaterBox

Five-site water box (TIP5P).

DischargedWaterBox

Water box test system with zeroed charges.

FlexibleDischargedWaterBox

Water box test system with zeroed charges.

GiantFlexibleDischargedWaterBox

Flexible water box.

DischargedWaterBoxHsites

Water box test system with zeroed charges and Lennard-Jones sites on hydrogens.

AlchemicalWaterBox

Water box test system where a single water molecule can be alchemically modified.

WaterCluster

Create a few water molecules in a harmonic restraining potential

Peptide and protein systems

AlanineDipeptideVacuum

Alanine dipeptide ff96 in vacuum.

AlanineDipeptideImplicit

Alanine dipeptide ff96 in OBC GBSA implicit solvent.

AlanineDipeptideExplicit

Alanine dipeptide ff96 in TIP3P explicit solvent..

DHFRExplicit

Joint Amber CHARMM (JAC) DHFR / TIP3P benchmark system with 23558 atoms.

LysozymeImplicit

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

SrcImplicit

Src kinase in implicit AMBER 99sb-ildn with OBC GBSA solvent.

SrcExplicit

Src kinase (AMBER 99sb-ildn) in explicit TIP3P solvent using PME electrostatics.

SrcExplicitReactionField

Flexible water box.

Complexes

HostGuestVacuum

CB7:B2 host-guest system in vacuum.

HostGuestImplicit

CB7:B2 host-guest system implicit solvent.

HostGuestImplicitHCT

Attributes:

HostGuestImplicitOBC1

Attributes:

HostGuestImplicitOBC2

Attributes:

HostGuestImplicitGBn

Attributes:

HostGuestImplicitGBn2

Attributes:

HostGuestExplicit

CB7:B2 host-guest system in TIP3P explicit solvent.

Polarizable test systems

AMOEBAIonBox

A single Ca2 ion in a water box.

AMOEBAProteinBox

PDB 1AP4 in water box.

Test system base classes

These are base classes you can inherit from to develop new test systems.

TestSystem

Abstract base class for test systems, demonstrating how to implement a test system.