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

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.

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.

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.