grompp should warn if .mdp define does nothing
Users sometimes misuse -DPOSRES_WATER for -DPOSRE_WATER, etc. and don't get the simulation they intended
Developers sometimes misuse -DDIHS for -DDIH, leading to tests that don't test dihedrals.
A helpful diagnostic for these cases would be that an .mdp whose include section defines something that was never used triggers a warning in grompp. Implementing that would require some basic parsing of that field for -D usage (or perhaps -I also), and something that bumps a counter when it parses an ifdef.
None of this should be done if we're switching to some new format for topologies and thus parsing, but we may not achieve that in practice for GROMACS 2017.
Whether in a new implementation or not, I further suggest that we drop the feature that lets you control the parsing of the topology from the .mdp file. Only having to update the equilibration.mdp file to produce the simulation.mdp file is convenient if you remember to do the right things, but clearly also brittle. pdb2gmx can just as easily write equilibration.top that has optional position restraints that users can turn on by editing the file. Having everything related to how the potential energy function works in the topology is conceptually attractive, but the only advantage I have thought of is usability. If so, the .mdp file is now clearly a higher-level thing that uses it.
Remove defines that tests don't intend to use
Implementing a check that mdrun will implement the simulation the user
asked for means we need our tests to specify their intent correctly.
Add grompp check for usage of "define" field in mdp
Users can misspell the strings specified with -D in the topology. This now
check that every -D field has a corresponding #ifdef and/or #ifndef and/or
C macro-style text replacement in the topology.
Fixed one unit test with unnecessary define field
#3 Updated by Kevin Boyd 8 months ago
I think this is worthwhile, even if our implementation changes in time for Gromacs 2020 - we could still put it in 2019.1 and 2018.x (or 2019, but IDK if something like this can go in so close to release). A check like this would have saved me some grief in the past.