gistfile1.txt

import mbuild
import foyer
import mosdef_cassandra as mc
import unyt as u
from mosdef_cassandra.utils.get_files import (
    get_example_ff_path,
    get_example_mol2_path,
)


def run_nvt_spce(**custom_args):

    # Load water with SPC/E geometry from mol2 file
    molecule = mbuild.load("O", smiles=True)

    # Create an empty mbuild.Box
    box = mbuild.Box(lengths=[3.0, 3.0, 3.0])

    # fill box
    water_box = mbuild.fill_box(molecule, n_compounds=1, box=box)

    # Load forcefields
    spce = foyer.Forcefield(get_example_ff_path("spce"))

    # Use foyer to apply forcefields
    molecule_ff = spce.apply(water_box)

    # Create box and species list
    box_list = [water_box]
    species_list = [molecule_ff]

    # Use Cassandra to insert some initial number of species
    mols_in_boxes = [[1]]

    # Define the system object
    system = mc.System(box_list, species_list, mols_in_boxes=mols_in_boxes,
            fix_bonds=True)
    # Get the move probabilities
    moveset = mc.MoveSet("nvt", species_list)

    default_args = {
        "angle_style": ["fixed"],
    }

    # Combine default/custom args and override default
    custom_args = {**default_args, **custom_args}

    # Run a simulation with at 300 K with 10000 MC moveset
    mc.run(
        system=system,
        moveset=moveset,
        run_type="equilibration",
        run_length=10000,
        temperature=300.0 * u.K,
        **custom_args,
    )


if __name__ == "__main__":
    run_nvt_spce()