Aggregation Analysis

This function calculates key quantities related to the aggregation process of a specific molecule type. All quantities are calculated as a function of simulation time. The relevant quantities recorded include the aggregation number, z-aggregation number, average radius of gyration, average relative shape anisotropy, and average estimate cluster density.

IMPORTANT NOTE: While the aggregation number is calculated for a selected group of molecules (as specified in the input), you can also specify a second group of molecules that act as inhibitors. The radius of gyration, shape anisotropy, and cluster density are calculated considering both the primary molecule group AND the inhibitors group TOGETHER. This approach helps overcome the limitations of the aggregation number analysis

For example, when studying the aggregation of molecules of type A, two aggregates of A might not interact directly but may be connected by one or more inhibitors, forming a larger cluster of A + inhibitors. In this case, the aggregation number would remain low because it only considers type A molecules. However, the radius of gyration would be large, alerting the user to the presence of a significant cluster involving both A and the inhibitors.

Allowed number of parents: 1