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In the context of drug discovery, computational methods were able to accelerate the challenging process of designing and optimizing a new drug candidate. Amongst the possible atomistic simulation approaches, metadynamics (metaD) has proven very powerful. However, the choice of collective variables (CVs) is not trivial for complex systems. To automate the process of CVs identification, we apply here two different machine learning (ML) algorithms, namely DeepLDA and Autoencoder, to the metaD simulation of a well‐researched drug/target complex, constituted by a pharmacologically relevant non‐canonical DNA secondary structure (G‐quadruplex) and a metallodrug acting as its stabilizer, as well as solvent molecules.

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