Example notebooks for carrying out various OpenFF tasks from the Shirts group.
- openff-POPC-am1bcc-nagl.ipynb: Shows molecule parameterization and charge calculation for POPC for both AM1-BCC and NAGL charges - AM1-BCC takes about 12 min, whereas NAGL takes ~1 sec (maybe 4 seconds first time called). Filed output in GROMACS.
- openff-molecule-output-lots-of-ways.ipynb: A bunch of ways to build systems, including a single molecule, many copies of the molecule packed in box, a molecule solvated in water, and three molecules in a mixture together in a box. Sample files in GROMACS, AMBER, and LAMMPS.