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grompp should warn if .mdp define does nothing - Redmine #1975

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 gromp 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.

(from redmine: issue id 1975, created on 2016-05-30 by mark.j.abraham, closed on 2019-06-02)

  • Changesets:
    • Revision e063041ed2c15ccce89496fd20700af7e5947102 by Mark Abraham on 2019-01-11T09:21:07Z:
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.

Refs #1975

Change-Id: I041c0342c02406c1a9899ee397af5ccfb012f9a4
  • Revision 2363b5ff by Kevin Boyd on 2019-01-13T13:38:37Z:
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

refs #1975

Change-Id: Ie6329b234a60dde8efc34fb788e6296f241651ed