On the one hand, the C/d approach (top) applies the Aggregate program to the snapshots generated along the MD trajectory. These snapshots typically contain aggregates of varying sizes, each spanning multiple interaction patterns. The Aggregate program identifies the size and interaction pattern of each aggregate, ultimately providing their populations. On the other hand, the Q/s approach (bottom), implies an initial systematic conformational search that generates isomers for aggregates of different sizes. The Aggregate program is subsequently run over these isomers to map them to their corresponding interaction-pattern conformers, and their populations are determined by accounting for the free energies of all isomers contributing to each interaction pattern.