A puzzle is a pretty good analogy for designing drug molecules. Drugs interact with proteins and enzymes much like trying to snap a puzzle piece into a puzzle. i.e lock and key model. Currently the strategy drug companies use essentially amounts to synthesizing millions of potential drug candidates in small quantities and testing for target activity. This is... horribly inefficient and it is hoped that better modeling can help cut down on either the number of candidate drugs that need to be screened and/or refine the drugs' activity to be more targeted (reduce side effects)

I am working toward submitting some of it for publication in a peer reviewed scientific journal. The research in question involves new aromatic ring systems that mostly have applications as catalysts.

Into lammps or in general? Because I havent really messed with LAMMPS so I wouldnt be able to reccommend resources for that yet. But if you mean in general, orca and gaussian are the easiest to use. Nwchem and gamess are a bit more obtuse with their documentation.

Chemcompute autogenerates input files and can be used to run simple calculations on a supercomputer but is limited to 1 hour with 1 core unless you are affiliated with their parner universities. In the latter case you can use up to 32 cores for longer periods of time. Currently it has support for gamess, tinker, jupyterhub, psi4 and namd: https://chemcompute.org/

ORCA has a wiki for input file documentation and use: https://sites.google.com/site/orcainputlibrary/visualization-and-printing

Avogadro, jmol and chemcraft are common drawing programs that can be used to draw molecules and visualize various properties. (ORCA uses .out as the extension of the output file, gaussian uses cube files and nwchem can be told to output data as cube files but again, is much more obtuse)

Avogadro manual: https://avogadro.cc/docs/ Nwchem:https://nwchemgit.github.io/Home.html Gaussian: https://gaussian.com/man/ Gamess: https://www.msg.chem.iastate.edu/gamess/documentation.html