README.md

Examples for openforcefield tools

Manifest

  • SMIRNOFF_simulation/ - simulation of a molecule in the gas phase with the SMIRNOFF forcefield format
  • SMIRNOFF_comparison/ - compare molecule energies from SMIRNOFF/OpenMM and AMBER
  • forcefield_modification/ - Jupyter notebook example of modifying a forcefield parameter and evaluating how it changes an energy
  • chemicalEnvironments/ - example and documentation of using chemical environment objects to manipulate environment being considered, generate example SMIRKS, etc. Also contains IPython notebook using the chemical environment for depiction.
  • mixedFF_structure - example of how to use SMIRNOFF forcefields for small molecules in combination with more conventional force fields for proteins and other components of your system.
  • partial_bondorder/ - example of using partial bond orders for parameterizing molecules, and showing how the SMIRNOFF format extends; see https://github.com/openforcefield/smarty/issues/53
  • host_guest_simulation/ - example of setting up a basic MD simulation for a host-guest system using the SMIRNOFF force fields.
  • label_molecule/ - example showing how to check which parameters are used in which molecules, do parameter usage statistics, etc.