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.
Create a 3D harmonic oscillator, with a single particle confined in an isotropic harmonic well. |
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Create a 3D Power oscillator, with a single particle confined in an isotropic x^b well. |
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Create a pair of particles in 3D harmonic oscillator wells, coupled by a constraint. |
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Create a 1D array of noninteracting particles in 3D harmonic oscillator wells. |
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Create an 'ideal gas' of noninteracting particles in a periodic box. |
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Molecular ideal gas (methanol box). |
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Create a free diatomic molecule with a single harmonic bond between the two atoms. |
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Create a system with an arbitrary number of CustomExternalForces. |
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A system of particles with a CustomGBForce. |
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Create a pair of Lennard-Jones particles. |
Clusters and simple fluids¶
Create a diatomic fluid. |
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Examples |
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Examples |
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Examples |
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Examples |
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Examples |
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Create a non-periodic rectilinear grid of Lennard-Jones particles in a harmonic restraining potential. |
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Create a periodic fluid of Lennard-Jones particles. |
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Lennard-Jones fluid with truncated potential (instead of switched). |
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Lennard-Jones fluid with switched potential (instead of truncated). |
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Create a periodic fluid of Lennard-Jones particles on a grid. |
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Create a periodic rectilinear grid of Lennard-Jones particles, but implemented via CustomBondForce and NonbondedForce. |
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Toluene GAFF/AM1-BCC in vacuum. |
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Toluene GAFF/AM1-BCC in implicit solvent. |
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Methanol box. |
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Create a few water molecules in a harmonic restraining potential |
Solids¶
Create an FCC crystal of sodium chloride. |
Water boxes¶
Create a water box test system. |
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Flexible water box. |
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Flexible water box using reaction field electrostatics. |
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Flexible water box using PME electrostatics and tight PME error tolerance. |
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Water box using PME electrostatics and tight PME error tolerance. |
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Flexible water box. |
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Four-site water box (TIP4P-Ew). |
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Five-site water box (TIP5P). |
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Water box test system with zeroed charges. |
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Water box test system with zeroed charges. |
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Flexible water box. |
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Water box test system with zeroed charges and Lennard-Jones sites on hydrogens. |
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Water box test system where a single water molecule can be alchemically modified. |
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Create a few water molecules in a harmonic restraining potential |
Peptide and protein systems¶
Alanine dipeptide ff96 in vacuum. |
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Alanine dipeptide ff96 in OBC GBSA implicit solvent. |
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Alanine dipeptide ff96 in TIP3P explicit solvent.. |
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Joint Amber CHARMM (JAC) DHFR / TIP3P benchmark system with 23558 atoms. |
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T4 lysozyme L99A (AMBER ff96) with p-xylene ligand (GAFF + AM1-BCC) in implicit OBC GBSA solvent. |
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Src kinase in implicit AMBER 99sb-ildn with OBC GBSA solvent. |
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Src kinase (AMBER 99sb-ildn) in explicit TIP3P solvent using PME electrostatics. |
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Flexible water box. |
Complexes¶
CB7:B2 host-guest system in vacuum. |
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CB7:B2 host-guest system implicit solvent. |
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CB7:B2 host-guest system in TIP3P explicit solvent. |
Polarizable test systems¶
A single Ca2 ion in a water box. |
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PDB 1AP4 in water box. |
Test system base classes¶
These are base classes you can inherit from to develop new test systems.
Abstract base class for test systems, demonstrating how to implement a test system. |