User defined molecule groups in topology section
Currently we have adopted a standard in the topology (atoms_group) with the following hierarchy: atoms-->monomers (if exist)-->monomer groups (if exist)--> molecules --> molecule groups, with molecule groups for each type of distinct molecule. We should also have support for user-defined molecule groups. A simple implementation would be that the user provides a yaml/json file with the desired group labels and molecule information (I guess atom indices in general) and group index (I guess this would also somehow need to be linked to a particular main file as well)...And then these custom molecule groups should added on top of the "parsed" molecule groups within the Atoms_group section.
@himanel1 , @ladinesa : Does something like this already exist, e.g., from the Area A/B work? Or do you see a relatively simple way to do this?