Add constrained minimization after the first epoch
Add constrained minimization after the first epoch

Add constrains in the minimizations after the first epochs in MD simulations.
The changes in this commit are made to reuse the minimization code from the
equilibration phase

AdaptivePELE/AdaptivePELE,AdaptivePELE/AdaptivePELE,AdaptivePELE/AdaptivePELE,AdaptivePELE/AdaptivePELE