OMSF Directory

Software Workflows Add your project!
Generating Partial Charges with the OpenFE CLI
Repo • Docs
Licenses: MIT

A tutorial on using the OpenFE CLI to generate partial charges.

Partial ChargeMolecular DynamicsPython
OpenFE Example: Relative Free Energies with the OpenFE CLI
Repo • Docs
Licenses: MIT

This tutorial will show how to use the OpenFE CLI to calculate free energies - with no Python at all!

Free Energy CalculationCLIPython
OpenFE Showcase: Relative Binding Free Energies in the TYK2 System
Repo • Docs
Licenses: MIT

A showcase of OpenFE for relative binding free energies from start to finish.

Free Energy CalculationPython
OpenFF Example: Combining a small molecule with Sage and a protein parameterized with an Amber protein force field
Repo
Licenses: MIT

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)

Protein-LigandSMIRNOFFAMBERPython
OpenFF Example: Conformer Energies
Repo
Licenses: MIT

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

Conformer EnergiesSmall MoleculesEnergy CalculationPython
OpenFF Example: Export OpenFF-generated OpenMM System to AMBER and GROMACS files
Repo
Licenses: MIT

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.

SMIRNOFFInterchangeAMBEROpenMMPython
OpenFF Example: Forcefield Modification
Repo
Licenses: MIT

Modify force field parameters and evaluate how system energy changes

Parameter ModificationEnergy EvaluationPython
OpenFF Example: Inspecting SMIRNOFF Parameters
Repo
Licenses: MIT

Inspecting which SMIRNOFF parameters are assigned to specific molecules

SMIRNOFFPython
OpenFF Example: QCArchive Interface
Repo
Licenses: MIT

Retrieve data from the QCArchive into Molecule objects

QCArchivePython
OpenFF Example: SMIRNOFF Simulation
Repo
Licenses: MIT

Simulation of a molecule in the gas phase with the SMIRNOFF force field format.

Gas Phase SimulationMolecular DynamicsPython
OpenFF Example: Virtual Sites Showcase
Repo
Licenses: MIT

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

SMIRNOFFVirtual SitesPython
OpenFF Example: Visualizations
Repo
Licenses: MIT

Shows how rich representation of Molecule objects work in the context of Jupyter Notebooks

VisualizationsJupyterPython
OpenFF Post Translational Modification Prototype
Repo
Licenses: MIT

A notebook to paramaterize and simulate PTMs using OpenFF

Gas Phase SimulationMolecular DynamicsPython
OpenFF Toolkit Showcase
Repo
Licenses: MIT

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

Molecular DynamicsProtein-LigandVisualizationJupyter NotebookPython