GROMACS 2021.4 release notes
----------------------------

This version was released on November 5th, 2021. These release notes
document the changes that have taken place in GROMACS since the
previous 2021.3 version, to fix known issues. It also incorporates all
fixes made in version 2020.6 and earlier, which you can find described
in the :ref:`release-notes`.

.. Note to developers!
   Please use """"""" to underline the individual entries for fixed issues in the subfolders,
   otherwise the formatting on the webpage is messed up.
   Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
   a space between the colon and number!

Fixes where mdrun could behave incorrectly
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Fixed crash for large system with virtual sites
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When large system with virtual sites were ran with domain decomposition
and OpenMP threading, mdrun would crash when the number of atoms in
a domain and its halo were more than 200000.

:issue:`4167`

Fixed bug with GPU LINCS occasionally shifting atoms in wrong direction
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Due to missing blocking synchronizations in the CUDA version of LINCS,
the shared memory was occasionally overwritten with the new data. This
may slightly affect the final coordinates of the shifted atoms.

:issue:`4199`

Disabled the use of PME Mixed mode for FEP simulations
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The use of Mixed mode PME (``-pme gpu -pmefft cpu``) led to incorrect
computation of :math:`{\frac{\partial V}{\partial {\lambda}}}` in FEP
simulations.

Mixed mode is only used when explicitly requested by the user.

:issue:`4190`

Fixed spurious nan in AWH free energy output when running FEP with other dimensions
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When running AWH with alchemical free energy perturbations as one of multiple dimensions
the free energy output could contain nan entries due to failing log operations. This did
not affect the AWH bias, which means that the simulations were not affected as such, but
the output was.

:issue:`4180`

Made mdrun work without MPI
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When configured with neither of MPI or thread-MPI, mdrun would terminate with an
assertion failure.

:issue:`4264`

Fixes for ``gmx`` tools
^^^^^^^^^^^^^^^^^^^^^^^

Fix ``gmx convert-tpr -s -o``
"""""""""""""""""""""""""""""

Formerly, this combination could be used when supplying an index file.
Now this combination can also be used with default index groups when
not supplying an index file.

grompp now prints a note again when combining center of mass motion removal and position restraints
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:issue:`4128`

Static selections of large index groups now work
""""""""""""""""""""""""""""""""""""""""""""""""

Commands like ``gmx distance -f traj.xtc -n ndx.ndx -select "group
\"Contacts\""`` only worked if the size of ``Contacts`` was less than
the number of atoms. This restriction was a bug, and has been fixed so
that ``Contacts`` make take any size.

Other similar uses of static selections derived from index groups will
also now work.

:issue:`4148`

Static selections of index groups with repeated indices now work
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Static groups from index files referenced in selections (e.g. ``gmx
tool -select "group \"Contacts\""``) only worked correctly if they
never had adjacent repeats of the same index within the
group. Repeating the same index can be meaningful e.g. in lists of
inter-atomic distances to analyze with ``gmx distance`` to analyze
``"1 2 2 3"``. Previously, the index group had to be written like
``"2 3 1 2"`` in order to work.

:issue:`4149`

Fixes that affect portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Miscellaneous
^^^^^^^^^^^^^

Fix a bug affecting re-run gmxapi scripts
"""""""""""""""""""""""""""""""""""""""""

A typo may have prevented gmxapi simulations from continuing from checkpoints
after being interrupted. Fixed in version 0.2.3 of the gmxapi Python package.

:issue:`4267`
