I am trying to sample a PDB with different restraints. I would like to
shuffle only some molecules, in order to have some of them in a fixed
position (the coordinates should not change after sampling). I define
these rigid particles as rigid bodies before shuffling
A rigid body is not fixed in space - it is merely constrained to move
rigidly. But excluded_rigid_bodies should prevent shuffle_configuration
from modifying those rigid bodies. My guess is that your
'fixed_particles' isn't really a list of RigidBody objects and so isn't
matching anything. I can't say for sure though without seeing a complete
working script.