Before embarking on generating a massively parallel MD dataset, it is crucial to carefully plan and consider several foundational aspects of MD simulations. First and foremost, the theoretical basis of your simulation must be established. Most biomolecular simulations sample the isothermic-isobaric "NPT" ensemble (constant number of atoms, pressure, and temperature), but other ensembles (e.b. NVE or NVT) can also be sampled. It is also important to choose an appropriate force field for the construct being simulated. Different force fields are optimized for different systems-proteins, nucleic acids, or small molecules -so choosing one that aligns with the biological system you are studying is key . Importantly, one must consider the A.