Choosing a subset of atoms to save Another important consideration is which atoms to save during the simulation. For some analyses, saving the positions of all atoms may be unnecessary, and focusing on just the atoms of interest (e.g. protein and ligand systems only) can significantly reduce storage needs. However, saving only a subset of atoms may limit the range of analyses that can be performed later (such as water networks), so this decision should be based on the anticipated downstream use of the data. This impacts both storage and frame collection frequency since selectively saving atoms can reduce the burden of frequent data collection. □ How many parallel replicates (same starting structures, different starting velocities) will be run?