6.4 Centroids

VEGA ZZ can manage pseudo-atoms whose coordinates are calculated in real time as symmetry center and are named centroids. A centroid can be used to measure distance, angle, torsion, angle between two planes as a normal atom. In molecular dynamics analyses, the centroid position is automatically recalculated for each frame.
To define a new centroid, you must select Edit Add Centroid in main menu:


Centroid dialog box


Picking the molecule atoms, whose maximum number is six (6), you can add a new centroid. The. Clicking New button,  a new centroid is added and clicking Reset button, the atom selection restarts from the beginning:

Centroid dialog box   Arrow  Centroid

Clicking Keep fixed checkbox, it's possible to fix the centroid coordinates, disabling the automatic update when the coordinates of the other atoms are changed (e.g. during trajectory analysis or torsion edit).
To close the dialog box, click Close and to remove all centroids, select Edit Remove Centroids. The centroids can be removed as normal atoms also. A typical application example could be the measure of the distance between two rings, as shown in the following picture: