GROMACS 2025.2 release notes
----------------------------

This version was released on May 12th, 2025. These release notes
document the changes that have taken place in |Gromacs| since the
previous 2025.1 version, to fix known issues. It also incorporates all
fixes made in version 2024.5 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
   a space between the colon and number!

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

Fix assertion failure with CUDA and HIP builds with empty domains
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

mdrun could exit with an assertion failure when a domain contained
zero atoms.

:issue:`5322`

Fix mdrun crashes with position restraints + flat-bottomed position restraints + p-coupling with COM refcoord-scaling + OpenMP
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

This combination can lead to (too) high position restraint forces when OpenMP
threads run slightly out of sync. Simulations will have very likely crashed
due to too high forces, unless they are very short.

:issue:`5337`

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

Fix parsing of pdb files with multiple cyclic and acyclic chains
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

pdb2gmx computed incorrect coordinate distances when checking for cyclicity
of the second and later chains in the pdb input file.

:issue:`5091`

grompp now warns about identical dihedraltype 9 definitions
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

grompp would silently ignore double, identical dihedraltype definitions with
function type 9. Now such entries are not ignored and a warning is generated.

:issue:`5333`

Fix out-of-boundary read in gmx sorient
"""""""""""""""""""""""""""""""""""""""

The outermost (maximum radius) bin in the histograms created for the -o and -no
output files from this tool added a value which was read from unallocated memory. Only
values in this bin were affected.

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

Fixed cross-test for Windows on Linux with Wine
"""""""""""""""""""""""""""""""""""""""""""""""

Cross-testing of |Gromacs| 2025.1 for Windows on Linux with Wine, by setting the
``CMAKE_CROSSCOMPILING_EMULATOR`` variable to ``wine`` or ``wine64``, could fail
due to our tests using CMake generator expressions and ignoring the variable
setting. The tests are now executed using the emulator set in the variable.

:issue:`5342`

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

Intel Xe2/Battlemage documentation
""""""""""""""""""""""""""""""""""

Expanded the documentation and rephrased a misleading error message.

:issue:`5330`

