BioSimSpace.Solvent

The Solvent package contains tools for solvating molecular systems.

Functions

solvate(model[, molecule, box, angles, ...])	Solvate with the specified water model.
spc([molecule, box, angles, shell, ...])	Add SPC solvent.
spce([molecule, box, angles, shell, ...])	Add SPC/E solvent.
tip3p([molecule, box, angles, shell, ...])	Add TIP3P solvent.
tip4p([molecule, box, angles, shell, ...])	Add TIP4P solvent.
tip5p([molecule, box, angles, shell, ...])	Add TIP5P solvent.
waterModels()	Return a list of the supported water models.

Examples

Print the list of supported water models.

import BioSimSpace as BSS

print(BSS.Solvent.waterModels())

Solvate a molecule in a 5 nanometer periodic box of TIP3P water with an ion concentration of 0.1 mol per litre.

import BioSimSpace as BSS

# Load a system and extract the first molecule.
molecule = BSS.IO.readMolecules("amber/ala/*")[0]

# Solvate the molecule.
solvated = BSS.Solvent.tip3p(
    molecule=molecule,
    box=3*[5*BSS.Units.Length.nanometer],
    ion_conc=0.1
)

The same as above, but instead passing “TIP3P” as an argument to the solvate function. This function should be used in any interoperable workflow Node where the water model is specified as an input requirement by the user.

import BioSimSpace as BSS

# Load a system and extract the first molecule.
files = BSS.IO.expand(BSS.tutorialUrl(), ["ala.top", "ala.crd"], ".bz2")
molecule = BSS.IO.readMolecules(files)[0]

# Solvate the molecule.
solvated = BSS.Solvent.solvate(
    "tip3p", molecule=molecule,
    box=3*[5*BSS.Units.Length.nanometer],
    ion_conc=0.1
)

Solvate the molecule with a shell of at least 2 nanometers of SPC water.

import BioSimSpace as BSS

# Load a system and extract the first molecule.
files = BSS.IO.expand(BSS.tutorialUrl(), ["ala.top", "ala.crd"], ".bz2")
molecule = BSS.IO.readMolecules(files)[0]

# Solvate the molecule.
solvated = BSS.Solvent.spc(
   "tip3p", molecule=molecule,
   shell=2*BSS.Units.Length.nanometer
)

Create a 50 angstrom periodic box of pure SPC/E water.

import BioSimSpace as BSS

water = BSS.Solvent.spce(box=3*[50*BSS.Units.Length.angstrom])