
GROMACS 2026.3 release notes
----------------------------

This version was released on June 25th, 2026. These release notes
document the changes that have taken place in |Gromacs| since the
previous 2026.2 version, to fix known issues. It also incorporates all
fixes made in version 2025.4 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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Avoid deadlock with NVSHMEM and ``GMX_DISABLE_STAGED_GPU_TO_CPU_PMEPP_COMM``
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Previously, |Gromacs| would freeze early on with this combination of
enabled features.

:issue:`5637`

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

Fix position restraint reference with pbc=xy and ref-coord-scaling=com
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

With pbc=xy and ref-coord-scaling=com, ``gmx grompp`` would incorrectly
subtract the COM of the restraint group from the z-component of the reference
coordinates. This should in most cases have caused obvious errors.

:issue:`5630`

Prevent buffer overflow in gmx angle
""""""""""""""""""""""""""""""""""""

Previously, if ``gmx angle`` was used to measure a dihedral, an internal loop
would execute exactly three times, regardless of how many angles were provided.
If fewer than three angles were provided, this led to a heap buffer overflow.

:issue:`5620`

Fix gmx anaeig -over when number of eigenvectors differs
""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Previously, ``gmx anaeig -over -v ev1.trr -v2 ev2.trr -first 1 -last 1``
would exit with a fatal error if the two eigenvector files contained a 
different number of eigenvectors.
Computing the subspace overlap of a set of eigenvectors should only require the 
two eigenvector files to have the same number of atoms, not the same number of 
stored eigenvectors. 

See also
`this discussion thread <https://gromacs.bioexcel.eu/t/gmx-anaeig-problematic-error-dimensions-in-the-eigenvector-files-dont-match/13427>`_


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

Fixed compilation error with Visual Studio and CUDA 13
""""""""""""""""""""""""""""""""""""""""""""""""""""""

Fixed compilation error with HeFFTe and NVHPC compiler
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Fixed gmxapi build failures with CUDA
"""""""""""""""""""""""""""""""""""""

In some configurations, building gmxapi could have failed with
``The link interface of target "Gromacs::libgromacs" contains: OpenMP::OpenMP_CUDA but the target was not found.``

:issue:`5656`

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

Update documentation and warnings in gmx angle
""""""""""""""""""""""""""""""""""""""""""""""

Previously, the documentation and warning messages did not specify specific
requirements to generate certain optional output files. Another warning message
suggests the user uses an option from the legacy version of the tool.
Documentation, warnings, and errors were updated for clarity.

:issue:`5625`
