import MDAnalysis
import numpy as np
from scipy.spatial.distance import euclidean

u = MDAnalysis.Universe('split_rhombic_small.gro')
residue = u.atoms.residues[0]
residue_centroid_no_pbc = residue.atoms.centroid(pbc=False)
residue_centroid = residue.atoms.centroid(pbc=True)
head_centroid_distance = euclidean(residue.atoms.positions[0],
        residue_centroid)
tail_centroid_distance = euclidean(residue.atoms.positions[-1],
        residue_centroid)
print 'residue_centroid no pbc:', residue_centroid_no_pbc
print 'residue_centroid:', residue_centroid
print 'head_centroid_distance:', head_centroid_distance
print 'tail_centroid_distance:', tail_centroid_distance