Ordered Clusters
Description
This node analyzes the aggregation of highly ordered molecules in a cluster, as happens with fatty acids. It applies a HDBSCAN algorithm to group molecules that are both spatially close and similarly oriented. The output will contain useful aggregation data as the number of clusters along the trajectory, the average number of molecules forming each cluster or the ratio of free molecules with respect to the total amount of molecules. Also, it is possible to visualize the clusters in the simulation cell through a 3D heat map analysis.
Latest version
Allowed number of parents: 1
| Parameter | Description | Value type | Value restrictions | Default value | Units |
|---|---|---|---|---|---|
Component name |
Component names of the group |
selector |
component types |
empty |
none |
Minimum molecules to form aggregate |
Minimum number of molecules to form an aggregate core |
integer |
> 0 |
30 |
none |
Stride |
Indicate the stride in the simulation for the aggregation analysis |
float |
≥ 0.0 |
0.0 |
ps |