This is part of the colvar module

Calculate the RMSD with respect to a reference structure.

REFERENCE	a file in pdb format containing the reference structure and the atoms involved in the CV.
TYPE	( default=SIMPLE ) the manner in which RMSD alignment is performed. Should be OPTIMAL or SIMPLE.

NUMERICAL_DERIVATIVES

( default=off ) calculate the derivatives for these quantities numerically

NOPBC

( default=off ) ignore the periodic boundary conditions when calculating distances

SQUARED

( default=off ) This should be set if you want mean squared displacement instead of RMSD