BioSimSpace.Solvent.spc

BioSimSpace.Solvent.spc(molecule=None, box=None, angles=[90.0000 degrees, 90.0000 degrees, 90.0000 degrees], shell=None, ion_conc=0, is_neutral=True, is_aligned=False, match_water=True, work_dir=None, property_map={})[source]

Add SPC solvent.

Parameters:

  • molecule (Molecule, Molecule, System) – A molecule, or container/system of molecules.

  • box ([Length]) – A list containing the box size in each dimension.

  • angles ([Angle]) – A list containing the angles between the box vectors: yz, xz, and xy.

  • shell (Length <BioSimSpace.Types.Length>`) – Thickness of the water shell around the solute. Note that the base length of the resulting box must be at least twice as large as the cutoff used by the chosen molecular dynamics engine. As such, the shell option is often unsuitable for small molecules.

  • ion_conc (float) – The ion concentration in (mol per litre).

  • is_neutral (bool) – Whether to neutralise the system.

  • is_aligned (bool) – Whether to align the principal axes of the molecule to those of the solvent box.

  • match_water (bool) – Whether to update the naming of existing water molecules to match the expected convention for GROMACS, which is used as the solvation engine.

  • work_dir (str) – The working directory for the process.

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

Returns:

system – The solvated molecular system.

Return type:

System