from MDAnalysis import *
import MDAnalysis.analysis
import numpy



def mindist(groupA,groupB):
    """ Returns minimum distance of two atomgroups """
    dists = MDAnalysis.analysis.distances.distance_array(groupA.positions, groupB.positions)
    return numpy.amin(dists)


u=Universe('test.gro','test.xtc')

for ts in u.trajectory:
    a=u.selectAtoms("resid 260")
    b=u.selectAtoms("resid 261")
    print mindist(a,b)