Patch for sander (AmberTools 14)

Tentative patch for sander.
It implements all features (including support for
MPI runs) except for replica exchange stuff.

Closes #106
Merge branch 'v2.1-sander' into v2.1
changelog
Amber can save originals

Since ambertools are released under the GPL 3 license, we can
store originals here. This is going to make future merges easier.
Merge branch 'v2.1'