awesome-python-chemistry VS lammps

Also I'd take a look through https://github.com/lmmentel/awesome-python-chemistry because I have a hard time believing this isn't a "solved problem" where you just need to find the right existing library.

This list of packages is probably a good place to start. It's a little unclear what your dataset looks like but at a guess you're going to need to parse molecular formulas and perhaps structures (you'll need to convert those into some machine-readable format like InChI). Sounds like you also need to consider molecular weight so you'll need a mass calculator if you don't have those values; you could build your own or leverage one of many available.

Look into verlet lists or cell lists for your task, which are typically used with a discrete element method such as LAMMPS for what you seem to be describing.

Your choices are an n-body simulation (e.g., LAMMPS) with Coulomb interactions or, if your electrons are sufficiently sparse, a particle-in-cell (e.g., Starfish). Your best bets for visualization are going to be matplotlib or something more user-friendly like Visit or Paraview. Without a neutralizing background, however, your electrons are just going to repel each other, hit the walls, and disappear - there's not going to be much interesting to visualize. What are you actually trying to simulate? With more information maybe you could receive some more targeted advice.

Is this just a personal /learning project? I see "chemical simulations" and think quantum-espresso, LAMMPS, NWChem, etc. If this is a personal project, I apologize for my bluntness above.

Actually, the LAMMPS website has a similar example: Just hover over the "LAMMPS" logo in yellow and blue.

Modify the file to add what you need. In your case, modify the post_force functions in the files, since those will allow you to define the integration steps for the Vicsek model and its variations.