Fixed the include path for ions.itp to start with the FF name.

Many of the test were using "#include "ions.itp" instead of
e.g. "gromos43a1.ff/ions.itp". The former will be deprecated and is
scheduled for removal in Change-Id I9c711b75f49.

Change-Id: Ifc1ffe326049dbc68525b929f42bede234865299