Setting positions from PLUMED

[GiovanniBussi]

We might consider allowing PLUMED to reset the positions stored in the MD code. Notice that:

• The MD code should be made aware of the change, so as to recompute neighbor lists etc
• Only "GROMACS-like" implementations, where all atoms are shared with PLUMED, could work. For "NAMD-like" implementations, where only requested atoms are passed, it might be more difficult.

I am interested in working on it, but it's low priority now.