Add NpT equilibration to BAP workflow

1. Add new bash script to run NpT equilibration,
2. Extend existing runBAPsimulations scripts with the ability to create .tpr files from the equilibrated structure before starting the simulation; also supply the .mdp file needed
3. Fix -noappend inconsistency in restartBAPsimulations scripts.

Only use the changes in this MR after implementing the changes suggested in changesToBeImplementedByCinecaNOW.txt!