Parallel Aggregation
Description
This node analyzes the aggregation of highly ordered molecules in a cluster, similarly to the Ordered Clusters node. However, instead of applying a clustering analysis it uses graph theory to find cores of molecules that fulfill certain restrictions. Three different restrictions are defined:
-
Maximum distance between the centers of mass of neighbor molecules in the same aggregate.
-
Maximum angle between the alignment vectors of neighbor molecules in the same aggregate.
-
Minimum number of molecules to form an aggregate.
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 number of free molecules along the analysis. Also, it provides a .zip file with .gro files containing all clusters obtained in the final frame of the 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 |
Maximum distance between centers of mass |
Maximum distance between the center of mass of neighbor molecules in a cluster |
float |
> 0 |
10.0 |
Å |
Maximum angle between molecules |
Maximum angle formed by neighbor molecules in a cluster |
floating-point number |
> 0.0 |
10.0 |
° |
Minimum molecules to form aggregate |
Minimum number of molecules to form an aggregate core |
integer |
> 0 |
10 |
none |
Stride |
Indicate the stride in the simulation for the aggregation analysis |
float |
≥ 0.0 |
10.0 |
ps |