testmodels

class ufedmm.testmodels.AlanineDipeptideModel(force_field='amber03', water=None, box_length=Quantity(value=25, unit=angstrom), constraints=HBonds, rigidWater=True)[source]

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

Keyword Arguments:

  • force_field (str, default="amber03") – The force field to be used for the alanine dipeptide molecule.

  • water (str, default=None) – The water model to be used if the alanine dipeptide is supposed to be solvated. Available options are “spce”, “tip3p”, “tip4pew”, and “tip5p”.

  • box_length (unit.Quantity, default=25*unit.angstroms) – The size of the simulation box. This is only effective if water is not None.

  • constraints (object, default=`openmm.app.HBonds`) – Specifies which bonds and angles should be implemented with constraints. Allowed values are None, openmm.app.HBonds, openmm.app.AllBonds, or openmm.app.HAngles.

  • rigidWater (bool, boolean=True) – Whether water molecules will be fully rigid regardless of the value passed for the constraints argument.

Variables:

  • system (openmm.System) – The system.

  • topology (openmm.app.Topology) – The topology.

  • positions (list of openmm.Vec3) – The positions.

  • phi (openm.CustomTorsionForce) – The Ramachandran dihedral angle \(\phi\) of the alanine dipeptide molecule.

  • psi (openm.CustomTorsionForce) – The Ramachandran dihedral angle \(\psi\) of the alanine dipeptide molecule.