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The distance calculations don't seem to be able to handle periodic boundaries, they probably should. Even with a centered and sane configuration, linalg.norm isn't going to give the minimum distance between two centers. One way of doing this would be mda.lib.distances.distance_array or mda.lib.distances.calc_bonds which will take a unitcell (box=) to given a minimum distance between two centers.
Maybe less importantly, calling center_of_geometry() isn't always going to give the real center if the atoms are split over a periodic boundary, eg if the atoms were all forced to be within the primary unit cell and the residue was bridging a box boundary.
The text was updated successfully, but these errors were encountered:
Hi @richardjgowers , thanks very much for this scientific input, indeed! I will look carefully into your suggested implementation in the following days and come back to this issue asap.
The distance calculations don't seem to be able to handle periodic boundaries, they probably should. Even with a centered and sane configuration,
linalg.norm
isn't going to give the minimum distance between two centers. One way of doing this would bemda.lib.distances.distance_array
ormda.lib.distances.calc_bonds
which will take a unitcell (box=
) to given a minimum distance between two centers.Maybe less importantly, calling
center_of_geometry()
isn't always going to give the real center if the atoms are split over a periodic boundary, eg if the atoms were all forced to be within the primary unit cell and the residue was bridging a box boundary.The text was updated successfully, but these errors were encountered: