protex.testsystems.setup_system

protex.testsystems.setup_system(psf: CharmmPsfFile, params: CharmmParameterSet, constraints=None, dummy_atom_type: str = 'DUMH', cutoff: float = 11.0, switch: float = 10.0, ensemble='nVT')[source]

Set up the OpenMM system.

Parameters:

  • psf (CharmmPsfFile) – The psf object.

  • params (CharmmParameterSet) – The force field parameters.

  • constraints = None – Which constraints should be applied. Currently, None and “Hbonds” are supported.

  • dummy_atom_type (str = “DUMH”) – Atom type of the dummy atoms.

  • cutoff (float = 11.0) – Cutoff distance for the nonbonded interactions (Angstrom).

  • switch (float = 10.0) – Start distance for switching for the nonbonded interactions (Angstrom).

  • ensemble = “nVT” – Ensemble to simulate in. Currently, “nVT” and “npT” are supported.

Return type:

The OpenMM system object.