GROMACS 2020.5 release notes
----------------------------

This version was released on TODO, 2020. These release notes
document the changes that have taken place in GROMACS since the
previous 2020.4 version, to fix known issues. It also incorporates all
fixes made in version 2019.6 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 redmine, without the
   a space between the colon and number!

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

Fix mdrun writing zero dH/dlambda and foreign lambda energies before checkpointing
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
With free-energy runs with separate-dhdl-file=no and nstdhdl not a multiple of
nstenergy, mdrun would write zeros for dH/dlambda and foreign energies to
the energy file for steps between the last energy frame and the checkpoint.
This would lead to errors in free-energy estimates which could go unnoticed
as values only deviate for a few steps.

:issue:`3763`

Fixed bugs with COM pulling and domain decompostion with weight or >32 ranks
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When using COM pulling and domain decomposition, the results would be
incorrect when using relative weights per atom or when using more than
32 DD MPI ranks. This would usually lead to crashes or obviously wrong
results.

:issue:`3750`

Fixed conserved energy for MTTK
"""""""""""""""""""""""""""""""

When using `pcoupl=MTTK` and `tcoupl=nose-hoover`, the calculated conserved
energy was incorrect due to two errors dating back to GROMACS 4.6 and 2018,
respectively. As a result, all reported conserved energies using this
combination of temperature and pressure coupling algorithms in any GROMACS
version since GROMACS 4.6 are likely to be wrong. Note that these errors did
not impact the dynamics, as the conserved energy is only reported, but never
used in calculations. Also note that this bug only affects this exact
combination of temperature / pressure coupling algorithms.

:issue:`3796`


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

Improve CHARMM support in gmx do_dssp
"""""""""""""""""""""""""""""""""""""

:issue:`3568`

Fix non-funtioning gmx h2order -d option
""""""""""""""""""""""""""""""""""""""""

The gmx h2order tool would always take the normal along the z-axis.

:issue:`3820`

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

Fix building on OSX
"""""""""""""""""""

The code wouldn't compile due to a missing include.

:issue:`3730`

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