For new learner

how can someone completely new to code, scripts, and simulations learn from the beginning

Enrol to a university and look for research groups doing molecular modelling. You most likely will find them in physics, chemistry (pharmacy), biology, and materials engineering departments.

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In case you don’t have access to an university or a research group, you can find a lot of beginner material online, see this page from the LAMMPS website.

Simon

edit: and this list of books too