Examples using SMIRNOFF with the toolkit

The following examples are available in the OpenFF toolkit repository. Each can be run interactively in the browser with binder, without installing anything on your computer.

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.