Topology-Handling

From wiki.gromacs.org

It will take some brainstorming to figure out the best way to resolve this.

Currently, restraints can be specified in the topology for each "molecule" section, and the restraints the atoms are applied to are indexed by the atom number as it shows up in the "atom" section of the topology. This means that it is impossible to apply angle/distance/dihedral restraints between atoms that are in different molecule sections. This is extremely inconvenient.

What's the best solution? To switch to allowing restraints to be specified using absolute atom numbering, as it appears in a gro file?