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The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases.

...More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be reimplemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.

...The codebase emphasizes readability and hackability so learners can modify the solver, add new behaviors, or swap integrators without wading through engine internals. It’s ideal when you want expressive motion and playful dynamics rather than full rigid-body simulation.