GROMACS 2021.1 release notes
----------------------------

This version was released on March 8th, 2021. These release notes
document the changes that have taken place in GROMACS since the
previous 2021 version, to fix known issues. It also incorporates all
fixes made in version 2020.6 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 GitLab, without the
   a space between the colon and number!

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

Fix MiMiC with virtual sites
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

It is likely that MiMiC with virtual sites has not worked
correctly because the call to construct the sites was placed
after the call that uses the sites. Now it should work, but we have not tested that it does.

:issue:`3866`

Fix mass perturbation to dH/dlambda
"""""""""""""""""""""""""""""""""""

The contribution for perturbed mass was missing in dH/dlambda.
Note that this contribution was not missing from the foreign energy
differences used for the Bennett acceptance ratio method.

:issue:`3943`

Running AWH with a convolved potential and an FEP dimension gives wrong results.
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

The output PMF is wrong when using awh-potential = convolved with a
pull dimension combined with an FEP dimension. The FEP dimension
always uses an umbrella potential and the combination does not work
properly. This has been disabled in grompp.

:issue:`3946`

Remove velocity from partially frozen atoms in md-vv
""""""""""""""""""""""""""""""""""""""""""""""""""""

md-vv would add some velocity to the frozen dimensions of partially
frozen atoms during constraining. This did not lead to wrong
trajectories, as the frozen dimensions of the positions are kept fixed
during propagation. The non-zero velocities were, however, reported in
trajectories and final configurations. They might also have lead to
slightly wrong kinetic energies, since the reported kinetic energy is
calculated after the velocities are constrained. All effects are
expected to be relatively small, since they did not accumulate, as the
velocities were regularly reset to zero once per step.

:issue:`3849`

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

Fix periodic boundary conditions in analysis framework tools
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

There was a bug in the trajectory analysis framework which caused
molecules that were broken over PBC not to be made whole. This would
usually lead to obviously incorrect outliers in analysis output.

:issue:`3900`

Fix range checking bug in ``gmx covar``
"""""""""""""""""""""""""""""""""""""""

A check was inverted causing range checking to be applied wrong.

:issue:`3902`

Fix various bugs in ``gmx xpm2ps``
""""""""""""""""""""""""""""""""""

Numerous minor issues were introduced in refactoring since
|Gromacs| 5.1, now fixed.

:issue:`3881`

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

Fixed compilation on Cygwin
"""""""""""""""""""""""""""

A |Gromacs| header file was not including the necessary standard
header. A problem with the ``M_PI`` math constant defined only by
POSIX and not by C++ was also worked around.

:issue:`3890`

Improve grompp checks of AWH settings when sampling an FEP dimension
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Ensure that the AWH sampling interval is compatible with nstcalcenergy
when sampling an FEP dimension using AWH. This avoids crashes in the
first AWH sampling step (step > 0) if the settings were not correct.

:issue:`3922`

Miscellaneous
^^^^^^^^^^^^^
* Updated |Gromacs| logos
