Pymatgen-IO-OpenMM

pymatgen-io-openmm makes setting up OpenMM simulations fast and easy.

The documentation is under active development. If you would like to use this package, please contact Orion Cohen so that he makes time to finish documenting and mint a PyPI release.

pymatgen-io-openmm is a pymatgen namespace package. You can install this package from source and all functionality will be available in the pymatgen namespace. A basic usage example is shown below.

from pymatgen.io.openmm.generators import OpenMMGenerator

# Create a generator object
generator = OpenMMGenerator()

input_mol_dicts = [
    {"smile": "O", "count": 200},
    {"smile": "CCO", "count": 20},
]

input_set = generator.get_input_set(input_mol_dicts, density=1)

simulation = input_set.get_simulation()
simulation.minimizeEnergy()
simulation.step(1000)

Developer Mode Installation Instructions

1. Install the conda package manager and create a fresh conda environment with python 3.10 or greater.

   conda create -n openmm python=3.10

2. Clone this repository and move into it.

   git clone [email protected]:orionarcher/pymatgen-io-openmm.git
   cd pymatgen-io-openmm

3. Install the requirements in requirements.txt.

   conda install -c conda-forge --file requirements.txt

4. Install the package in editable mode.

   pip install -e .

Installing on Apple Silicon

If you are using Apple Silicon, installation is a bit trickier. Some dependencies of OpenFF are not compatible with Apple Silicon so you will need to use Rosetta 2. First open your terminal application with Rosetta2 enabled, then create a conda environment following these instructions everything should work from there. This replaces step 1. Do not use mamba, which is not fully integrated with x86 installations for Apple Silicon.

Running tests

To run the testing suite, run following commands from the root of the repository and with your conda environment activated:

cd /pymatgen/io/openmm/tests
pytest .

Data files paths within the testing suite assuming a path relative to pymatgen/io/openmm/tests.