Molecular Dynamics Component

This is part of the MolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides a Tactic component for mmic_md using the Gromacs software suite

Preparing Input

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

# Import Strategy MD component
import mmic_md
# Import Tactic MD component 
import mmic_md_gmx

# Construct molecule and forcefield objects
# If a specific translator is impoted, it can be used with  
# mol = Molecule.from_file(path_to_file, TRANSLATOR_NAME)
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(
	engine="gmx", # Engine must be gmx and must be specified
    schema_name=SCHEMA_NAME,
    schema_version=SCHEMA_VERSION,
    system={mol: ff},
    boundary=(
        "periodic",
        "periodic",
        "periodic",
        "periodic",
        "periodic",
        "periodic",
    ),
    max_steps=TOTAL_STEP_NUMBER,
    step_size=STEP_SIZE,
    method="md",
    freq_write={"nstxout": 5, "nstvout": 5, "nstenergy": 5, "nstlog": 5},
    long_forces={"method": METHOD_FOR_LONGRANGE_INTERACTION},
    short_forces={"method": METHOD_FOR_SHORT_INTERACTION},
    temp_couple={"method": T_COUPLE_METHOD, "ref_t": REFERENCE_T},
    press_couple={"method": P_COUPLE_METHOD},
)	

Examples for the Parameters:

METHOD_FOR_LONGRANGE_INTERACTION "PME"

METHOD_FOR_SHORT_INTERACTION "cut-off"

T_COUPLE_METHOD "Berendsen"

P_COUPLE_METHOD "Parrinello-Rahman"

Runing MD Simulation

# Import strategy compoent for runing MD simulation
from mmic_md_gmx.components import MDGMXComponent

# Run MD Simulation
outp = MDGMXComponent.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.