Fix mdrun-only build

Fix mdrun-only build

The GMX_BUILD_ONLY_MDRUN build now does not include
the gmxpreprocess module. Some Verlet-scheme code moved
to mdlib because it it used in mdrun and grompp.

gmx membed uses a utility function otherwise used only in
gmxpreprocess, but the error message it gives is wrong for the gmx
membed context, so I duplicated the function definition for now. Noted
TODOs for future clean up.

Fixes #1683

Change-Id: Ibc1291e88151f8d5befac2b1840a41402272a05f