Constraints and Restraints

In GROMACS, "constraints" and "restraints" refer to different simulation processes. Constraints are used to fix the length of (a subset of) bonds after the integration of forces. Restraints come in a number of flavours, and involve perturbing the Hamiltonian so that the ensemble it produces fits some preconceived notion, such as implementing an energy penalty for deviating from a defined value (in the case of atomic positions, dihedral angle, etc).  See the GROMACS Manual for more information.