GROMACS 2022.2 release notes
----------------------------

This version was released on June 16th, 2022. These release notes
document the changes that have taken place in GROMACS since the
previous 2022.1 version, to fix known issues. It also incorporates all
fixes made in version 2021.5 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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Fix incorrect constraining in highly parallel runs
""""""""""""""""""""""""""""""""""""""""""""""""""

With domain decomposition, OpenMP and connected constraints (so not only
bonds with hydrogens constrained), constraint correction could be applied
when a domain would not have any constraints while it had constraints before.
This is unlikely to have gone unnoticed in longer runs, as the chance is
high that atoms would clash and the system would become unstable. But short
runs might not crash and could therefore produce incorrect results. The correctness can
be judged from the drift in the conserved energy quantity, which is reported
at the end of the log file, and which will be one to two orders of magnitude
larger than for a correct run.

:issue:`4476`

Fix missing CPU-GPU synchronization when doing free-energy calculations
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When GPU halo exchange with direct communication is enabled, CPU based 
free-energy kernels were being run without waiting on non-local co-ordinates 
to be available on host. This resulted in use of stale data on CPU side. 
This issue can cause incorect output when GPU direct communication is enabled 
using GMX_ENABLE_DIRECT_GPU_COMM environment variable and simulation contains 
free-energy calculations.

:issue:`4471`

Fix missing PME mesh dV/dlambda with PME on GPU on a seperate PME rank
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When doing free-energy calculations with PME running on GPU on a separate
PME rank, the dV/dlambda contribution for the PME mesh part was missing.
The same contribution was missing from the foreign lambda energy differences.
Note that the energies and forces were correct.

:issue:`4474`

Removed the (incorrect) output file size note/warning with mdrun -rerun
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

:issue:`4484`

Wait for PME coordinate padding clearing to complete after reinitialization
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

As part of the irregular reinitialization of PME coordinate buffers,
the padding area of the buffer on the GPU must be set to
zero. Previously, a dependency was missing such that, with GPU direct
communications enabled via the GMX_ENABLE_DIRECT_GPU_COMM, it was
possible that the PME kernel could preceed before this initialization
had completed, and this has now been fixed. The incorrect ordering is
only expected to have occured in extreme benchmarking cases, causing
an obvious crash.

:issue:`4482`

Note known issues with Verlet buffer estimation
"""""""""""""""""""""""""""""""""""""""""""""""

There are known issues with the Verlet buffer estimate for imhonogeneous
systems as well as for potentials with only the repulsive part of the
Lennard Jones potential. These issues and workarounds are listed in
the :ref:`known issues <gmx-users-known-issues>` section.

:issue:`4509`

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

Clarified pdb2gmx error message for undefined atom type in terminal database
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

:issue:`4481`

Lower severity of grompp exclusion distance issues with energy minimization
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

With energy minimization, the error/warning about pair distances
beyond/close to the cut-off has been changed to a warning/note,
as energy minimization might fix such issues.

:issue:`4480`

Fixed missing cmap torsion correction for periodic pepdites
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When using pdb2gmx with periodic peptides and the CHARMM27
force field, the CMAP correction across the periodic boundary
was missing (but not the torsion itself). Reprocess your
PDB file with pdb2gmx from version 2022.2 or later to get a
correct topology, or add it manually to the topology.

Avoid crash in gmx bar with invalid input
"""""""""""""""""""""""""""""""""""""""""

gmx bar could try to read an invalid input data file and would fail with a hard
crash instead of a helpful error message.

Fix printing of incorrect data from analysis tools
""""""""""""""""""""""""""""""""""""""""""""""""""""

A change on how we handle selections caused the analysis tools in the
trajectoryanalysis framework to print data for wrong selections.

:issue:`4508`

Remove broken charge zeroing function in convert-tpr
""""""""""""""""""""""""""""""""""""""""""""""""""""

This had been broken for a long time and no discernable use.

:issue:`4226`


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

Warn when using gcc version 7 with CUDA builds
""""""""""""""""""""""""""""""""""""""""""""""

Different versions of gcc 7 behave differently in a way that makes it
hard for |Gromacs| to check whether CUDA's ``nvcc`` compiler will
accept compiler flags. |Gromacs| 2022 and 2022.1 sometimes would
spuriously detect flags as invalid, avoid using them, and so produce
slow CUDA kernels. Now |Gromacs| assumes all nvcc flags are valid in
this case and the build system warns when this is occuring. If you
then experience build failures, please use a newer version of gcc.

:issue:`4478`

Fix external tinyXML version to below 7
"""""""""""""""""""""""""""""""""""""""
Newer versions are not compatible with |Gromacs|.

:issue:`4477`

Fixed a possible software build error with OpenMP linking
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""

In some situations, software builds could have errors linking ``omp`` symbols.
A minor update to the CMake configuration helps the ``muparser`` component
to find the same OpenMP dependency used by the rest of the library.

:issue:`4499`

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

Fixed detection of external TinyXML-2
"""""""""""""""""""""""""""""""""""""

Updated the code to properly detect the presence and the version of external
TinyXML-2 (only relevant if ``-DGMX_EXTERNAL_TINYXML2=ON`` is used).

:issue:`4477`

Fixed warnings when using module-specific OpenMP thread-count environment variables
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

One of the arrays used to construct message strings wasn't updated
properly, so sometimes an information message was wrong or may have
printed garbage.
