GROMACS 2024.1 release notes
----------------------------

This version was released on February 28th, 2024. These release notes
document the changes that have taken place in |Gromacs| since the
previous 2024.0 version, to fix known issues. It also incorporates all
fixes made in version 2023.4 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 rounding errors with Parrinello-Rahman coupling of triclinic boxes
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

With triclinic boxes and isotropic or diagonal Parrinello-Rahman pressure
coupling, the off-diagonal scaling matrix arguments could be non-zero.
This was harmless, apart from causing an assertion failure when update
was executed on a GPU.

:issue:`4974`

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

Fixed parsing of phases in gmx nmtraj
"""""""""""""""""""""""""""""""""""""

:issue:`4968`

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

Fix compiler flag check with oneAPI DPC++
"""""""""""""""""""""""""""""""""""""""""

Some compiler warning flags were not tested properly when compiling for
NVIDIA/AMD GPUs using Intel oneAPI. No user-facing impact expected.

:issue:`5005`

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

Address mdrun performance regression with non-bonded interactions on CPU
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

The heuristics for choosing the inner pair-list interval has been
improved to regain or improve the performance on non-bonded interactions
on the CPU. Correctness is unaffected.

:issue:`4988`

Fixed nbnxm-test failure when bounds checking was enabled for stdlib
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

:issue:`4966`
:issue:`4973`

Increase tolerance of mdrun continuation tests in double precision
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

The mdrun continuation tests could fail in double precision with
errors just above the tolerance.

:issue:`4788`
:issue:`4931`

Fix missing OpenMP initialization in grompp
"""""""""""""""""""""""""""""""""""""""""""

The problem only manifested as a pop-up message when running
``gmx grompp`` built with Visual Studio. Since this message was
blocking the application, it could mess up with test suite
or automated scripts. No other deleterious effects noted.

:issue:`4961`

Fix grompp & mdrun crash when GMX_USE_COLVARS=NONE
""""""""""""""""""""""""""""""""""""""""""""""""""

Colvars MDModule was not properly constructed when the Colvars
library was not compiled. Colvars mdp fields handler was returning
a nullptr.

:issue:`4980`

Fix broken completion script on zsh-5.9 (Mac OS Sonoma)
"""""""""""""""""""""""""""""""""""""""""""""""""""""""

The compinit command must be loaded by the script before
loading bashcompinit, or there will be an error message
when sourcing GMXRC on some zsh versions.

:issue:`4986`
