Dear Mr. Alwera,

it depends totally on what you want to study on the atomic scale. You should specify your question in more detail.

If the interaction of atoms on a bigger scale (several 10 nm to microns) is of interest, molecular dynamics (Short: MD in literature) simulations usually are the simulation tool of choice.

If the electronic structure needs to be involved and only a few atoms need to be simulated, you should take into account ab-initio simulations such as density-functional theory (DFT).

Furthermore, it is possible to get a mixture of both worlds, which is known as ab-initio molecular dynamics.

Best regards

Daniel Foerster

https://link.springer.com/content/pdf/10.1007/978-3-642-18369-0_12.pdf

You may go through the following article

Article Open Source Molecular Modeling