Inconsistent graph PBC results with monomers connected by restraints
The graph code implicitly assumes that the bonded interactions connecting atoms in a moleculetype a short-ranged compared to the box size. But this is not necessarily the case when multiple monomers in a single moleculetype are connected by restraints. Such restraints can work over more than half the box length. In the current code this can lead to monomers being broken over PBC.
The least we should do is add a check for this, but this might be computationally expensive and/or complicated. The solution for the user would then be to increase the box size.
Ideally we would want a solution, but that can only be done through allowing the user to specify how the monomers should be connected.
Add fatal error for inconsistent graph
In case a moleculetype consists of multiple monomers connected
by restraints, an inconsistent graph could be generated.
Now a fatal error with explanation is generated for such cases.
Also a fatal error is generated with an inconsistent graph with long
bonds in general.