Move the run of PELE equilibration to new function
Move the run of PELE equilibration to new function

The changes in the runSimulation method broke the PELE equilibration, move the
run to a new function

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