GROMACS 2019.3 release notes
----------------------------

This version was released on June 14, 2019. These release notes
document the changes that have taken place in GROMACS since the
previous 2019.2 version, to fix known issues. It also incorporates all
fixes made in version 2018.7 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 missing interactions with domain decomposition
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When running with domain decomposition, any interactions described by
the rarely-used topology file section
``[ intermolecular_interactions ]`` were ignored. This did not
affect normal non-bonded or intra-molecular interactions.

:issue:`2953`

Fix possible floating point exception during minimization.
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

It was possible that very small forces during minimization could lead to
a crash due to a divide by zero error. Fixed by introducing a check.

:issue:`2917`

Fix segmentation fault when using membrane embedding
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

:issue:`2947`

Allow AWH with pull-geometry 'direction' to be periodic
"""""""""""""""""""""""""""""""""""""""""""""""""""""""

When applying AWH to a pull coordinate with geometry 'direction'
with a AWH interval length of more than 95% of the box size,
the dimension is now made periodic.

:issue:`2946`
       
Fixes for ``gmx`` tools
^^^^^^^^^^^^^^^^^^^^^^^

Fixed residue and molecule indexing in selections
"""""""""""""""""""""""""""""""""""""""""""""""""

:issue:`2951`

Fix PQR formatting
""""""""""""""""""""

The formatting was incorrect for some tools that use PQR files.

:issue:`2955`

Fix gmx wham with angle geometries
""""""""""""""""""""""""""""""""""

gmx wham would mix up degree and radian units leading to no overlap
or not-a-number output. **Note**: this fix is not correct, a correct
fix is applied in the next patch release.

:issue:`2609`
:issue:`3094`

Add some information for grompp error with wrong line endings
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Give meaningful error with too large grid in hbond
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When using a grid that is too large :ref:`hbond <gmx hbond>` could try to
allocate enough memory to cause a crash.

:issue:`2962`

Add some information for syntax errors with include delimiters in grompp
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

:issue:`2911`

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

Fixed wider reference SIMD setups
"""""""""""""""""""""""""""""""""

The reference SIMD builds could use a too small memory alignment,
leading to mdrun exiting with an alignment error

:issue:`2952`

Fixed build failure with Apple Clang
""""""""""""""""""""""""""""""""""""

Builds would fail because of qsort being undefined.

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

Removed non-existent mdp option awh1-dim1-period from user guide
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

:issue:`2940`

Add checks for too many interactions during memory allocation
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

:issue:`2932`

