MINT

Molecular Dynamics Component

This is part of the MolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides a strategy component for running Molecular Dynamics simulations for systems composed by molecules and their forcefields.

Preparing Input

# Import moleucule and forcefield models
from mmelemental.models import Molecule, ForceField

# Import MD component
import mmic_md

# Construct molecule and forcefield objects
mol = Molecule.from_file(path_to_file)
ff = ForceField.from_file(path_to_file)

# Construct input data model from molecule and forcefield objects
inp = mmic_md.InputMD(
    schema_name=SCHEMA_NAME,
    schema_version=SCHEMA_VERSION,
    system={mol: ff},
    ...
)	

Runing MD Simulation

# Import strategy compoent for runing MD simulation
from mmic_md.components import MDComponent

# Run MD Simulation
outp = MDComponent.compute(inp)

Extracting Output

# Extract the potential energy 
pot_energy = outp.observables["pot_energy"]
...

Copyright

Copyright (c) 2021, Xu Guo, Andrew Abi-Mansour

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 0.0.