testmodels

class openxps.testmodels.AlanineDipeptideModel(water_model=None, number=500)[source]

A model consisting of a single alanine-dipeptide molecule, either in a vacuum or solvated in explicit water.

Parameters

  • water_model (Optional[str]) – the water model to be used. If this is None, then the alanine dipeptide will be simulated in a vacuum. Available options are “spce”, “tip3p”, “tip4pew”, and “tip5p”.

  • number (Optional[int]) – the number of water molecules to be added if water_model is not None.

Variables

  • topology (openmm.app.Topology) – The Topology of the alanine dipeptide model

  • positions (list[openmm.Vec3]) – The positions of all alanine dipeptide and water (if any) atoms

  • phi (CollectiveVariable) – The Ramachandran dihedral angle \(\phi\) of the alanine dipeptide molecule

  • psi (CollectiveVariable) – The Ramachandran dihedral angle \(\psi\) of the alanine dipeptide molecule

Examples

>>> import openxps as xps
>>> model = xps.AlanineDipeptideModel()
>>> model.phi
phi: CustomTorsionForce (period=6.283185307179586 rad)

>>> import openxps as xps
>>> model = xps.AlanineDipeptideModel(water_model='tip3p')
>>> model.topology.getNumAtoms()
1522