Dear Steve and Axel,
thanks, that was helpful, really appreciate your dedicated services to the lammps community. I would like to add a thing here in case someone finds this discussion useful. For minimization with box relax, I checked the symmetry the way BKS ( http://doi.org/10.1103/PhysRevLett.64.1955 ) did, i.e., by calculating the internal parameters. One can find the equations needed to determine the internal parameters here: http://doi.org/10.1103/PhysRevB.46.1 . Thanks.
…or use one of those RMSD fit and alignment tools that people in
biosimulations use to determine how much (and where) their protein
structure has changed.