i have a tetramer protein with one calcium ion bound to each monomer. I have started the production run without any restraint at first, however, the ions left their binding site. So i added a restraint during the two equilibration stages but the same thing happened in the production run. So i was thinking about adding restraint on the ions during the production run. Is it correct to do so?

the ions are not present in the active site, but it was determined experimentally that the ions are important for the function of the protein.