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
objectsforcefield_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.