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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)
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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)
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