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.

.. _deprecated-functionality:

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(unpublished results), were never well tested, are not widely used,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.
