Calculate distance between periodic images

[H-EKE]

Hi,

I ran a MD simulations where I have a huge conformational change. I am worried that my inital box guess was too short, and now the periodic images are interacting between them. Is there a way to check if the protein is interacting whith its periodic image in MDAnalysis?

I thought about something like this, but Im not sure what to put as second selection (protein2)

import MDAnalysis as mda
from MDAnalysis.analysis import distances

u = mda.Universe('structure.psf', 'output.xtc')

protein = u.select_atoms('name CA') 
protein2 = u.select_atoms('name CA',periodic=True) 
distance_array = distances.distances_array(protein.positions, protein2.positions, box=u.dimensions)

[orbeckst]

The periodic=True does not do anything for atomgroups.

I don't think that there's a built-in way to do exactly what you want in MDAnalysis. However, we do have the MDAnalysis.lib.distances.augment_coordinates() function. You might be able to generate copies and then compute distances to the copies. Not sure how to do it in detail but this may at least be a starting point.

[H-EKE]

Dear @orbeckst

I will try your suggestion. Thanks a lot !