Task #2569

Updated by Mark Abraham over 1 year ago

Suggestions for functionality to announce as deprecated, either deprecate, to remove or replace at some later time.

Several of these are intended to clarify what combinations of things are actually supported in mdrun, simplifying its documentation challenge. Many things have custom input and output files, and we are a long way from all-works-with-all support. Many of the current decisions date from the time when we did not want to increase our install footprint of 80+ tools.

Current list:
* aromatic vsite construction in pdb2gmx
* @gmx mdrun -rerun@ (replace with @gmx rerun@ and @gmx tpi@; see also #1868)
* @gmx mdrun -membed@ (replace with @gmx membed@; we had the old @g_membed@, whose implementation we fixed, but the distinct tool is useful)
* non-integrators in the integrator .mdp option (replace with @gmx em@ along with an mdp option to choose an EM flavour; @gmx nm@)
* @gmx mdrun -gcom@ (need freedom to refactor integrators, and hopefully remove the motivation for this option; see also #1925)
* Benchmarking functionality (@gmx mdrun -nsteps n -resetstep x -resethway@ are not something normal mdrun users should use, and creates questions about @gmx mdrun -c confout.gro@ and checkpointing; whereas @gmx benchmark@ has a clear use and more options for implementations)
* Aspects of @editconf@, @trjconv@, @eneconv@ and @trjcat@ that belong as separate tools (e.g. @convert@ @renumber@ @cat@ @subsample@ @demux@)
* @gmx do_dssp@ (at some point we will want to reimplement this natively)

We should also have a docs page for all features that are deprecated, along with the version in which they got that status. Release notes will record when they were removed.