Added check in grompp for shells and inputrec issues.

Some combinations of inputrec settings do not work with shells,
in particular nstcalcenergy > 1 or use of a twin range cutoff.
This is now checked for in grompp. Fixes #1376.

Change-Id: I4382bcf5231920b22c725a7cf8e7b4e17c2526d9