gmx_bool bShakeOnly,gmx_bool bSettle);
/* Build a graph from an idef description. The graph can be used
* to generate mol-shift indices.
+ * at_start and at_end should coincide will molecule boundaries,
+ * for the whole system this is simply 0 and natoms.
* If bShakeOnly, only the connections in the shake list are used.
* If bSettle && bShakeOnly the settles are used too.
*/