feat: add md stability benchmark

[lwehrhan]

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Summary

This benchmark tests if an MLIP can run stable simulations of various organic small molecules and peptides (in vacuum and in solution), as well as of a protein in vacuum.

Linked issue

Resolves #640

Progress

• Calculations
• Analysis
• Application
• Documentation

Testing

New decorators/callbacks

[joehart2001]

Hi @lwehrhan, from a brief look this is looking nice and i think wont need many comments from us. Could you please take a look at the element filtering mentioned by @ElliottKasoar in #429, it should be pretty straightforward to add. then we will take a deeper look over. thanks!

[ElliottKasoar]

Does the benchmark save anything in terms of the trajectories? It might be interesting to see, for example, how far a simulation gets before exploding, even if it doesn't form a part of the score.

Either through that, or otherwise, it might also be nice to be able to see which systems were successfully simulated or not. Do you think this might be possible?

[joehart2001]

Thanks for the pr! same as #658 could you send the data + have a look at the element filtering?

docs: https://ddmms.github.io/ml-peg/developer_guide/filter.html