Deprecated functionality ------------------------ Changes anticipated to |Gromacs| 2019 functionality ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ``gmx mdrun -membed`` """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The feature for embedding a protein in a membrane will be retained, but probably in a different form, such as ``gmx membed``. ``gmx mdrun -rerun`` """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The feature for computing potential energy quantities from a trajectory will be retained, but probably in a different form, such as ``gmx rerun`` and ``gmx test-particle-insertion``. Integrator .mdp options will only contain dynamical integrators """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Energy minimization will be accessed in a differt form, perhaps with ``gmx minimize`` and interpret an .mdp field for which minimizer to use. Normal-mode analysis may be accessed with e.g. ``gmx normal-modes``. The command-line help for these tools will thenx be better able to document which functionality is supported when. Much functionality in ``trjconv``, ``editconf``, ``eneconv`` and ``trjcat`` """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The functionality in such tools is being separated to make it available in composable modules, that we plan to make available as simpler tools, and eventually via the |Gromacs| API that is under development. ``gmx do_dssp`` to be replaced """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This tool is deprecated, because it is problematic for some users to obtain and install a separate DSSP binary, so we plan to replace the implementation at some point with a native implementation, likely based upon xssp, and make it available under a new gmx tool name. Functionality deprecated in |Gromacs| 2019 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Generation of virtual sites to replace aromatic rings in standard residues """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" :issue:`3254` These are thought to produce artefacts under some circumstances (unpublished results), were never well tested, are not widely used, and we need to simplify pdb2gmx. ``gmx mdrun -gcom`` """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This feature sometimes overrides the effects of various .mdp settings in a way that is difficult to understand and report. A user who wants to do communication between PP ranks less often should choose their ``nst*`` mdp options accordingly. Benchmarking options only available with ``gmx benchmark`` """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" :issue:`3255` Options such as ``-confout``, ``-resethway``, ``-resetstep`` are not intended for use by regular mdrun users, so making them only available with a dedicated tool is more clear. Also, this permits us to customize defaults for e.g. writing files at the end of a simulation part in ways that suit the respective mdrun and benchmark use cases, so ``-confout`` will no longer be required. ``gmx mdrun -nsteps`` """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" :issue:`3256` The number of simulation steps described by the .tpr file can be changed with ``gmx convert-tpr``, or altered in .mdp file before the call to ``gmx grompp``. The convenience of this mdrun option was outweighted by the doubtful quality of its implementation, no clear record in the log file, and lack of maintenance. Functionality deprecated before |Gromacs| 2019 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ This functionality has been declared as deprecated in previous versions of |Gromacs|, but has not yet been removed. The group cutoff scheme """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" All remaining aspects of the group cutoff scheme will be removed, once a few remaining features (e.g. tabulated interactions, energy-group exclusions, and vacuum simulations) are available with the Verlet scheme. Deprecated in |Gromacs| 5.1 QM/MM support for ORCA, GAMESS and MOPAC """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" These interfaces are untested, and no maintainer has been found for them. Deprecated in |Gromacs| 2018.