Examples using SMIRNOFF with the toolkit

For users: These examples are best viewed at our centralized documentation page, where you will find a variety of ways to view and run the notebooks.

For developers: The following examples live in the OpenFF toolkit repository.

Index of provided examples

  • toolkit_showcase - parameterize a protein-ligand system with an OpenFF force field, simulate the resulting system, and visualize the result in the notebook

  • forcefield_modification - modify force field parameters and evaluate how system energy changes

  • conformer_energies - compute conformer energies of one or more small molecules using a SMIRNOFF force field

  • SMIRNOFF_simulation - simulation of a molecule in the gas phase with the SMIRNOFF force field format

  • vsite_showcase - two examples of using SMIRNOFF force fields virtual sites - a ligand with virtual sites on sulfure and chlorine and a comparison between the SMIRNOFF and OpenMM implementations of TIP5P

  • QCArchive_interface - retrieving data from the QCArchive into Molecule objects

  • forcefield_modification - modify force field parameters and evaluate how system energy changes

  • using_smirnoff_in_amber_or_gromacs - convert a System generated with the Open Force Field Toolkit, which can be simulated natively with OpenMM, into AMBER prmtop/inpcrd and GROMACS top/gro input files through the ParmEd library.

  • swap_amber_parameters - take a prepared AMBER protein-ligand system (prmtop and crd) along with a structure file of the ligand, and replace ligand parameters with OpenFF parameters.

  • inspect_assigned_parameters - check which parameters are used in which molecules and generate parameter usage statistics.

  • using_smirnoff_with_amber_protein_forcefield - use SMIRNOFF parameters for small molecules in combination with more conventional force fields for proteins and other components of your system (using ParmEd to combine parameterized structures)

  • visualization - shows how rich representation of Molecule objects work in the context of Jupyter Notebooks.