GROMACS 2019.2 release notes
----------------------------

This version was released on April 16th, 2019. These release notes
document the changes that have taken place in GROMACS since the
previous 2019.1 version, to fix known issues. It also incorporates all
fixes made in version 2018.6 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 L-BGFS minimizer
""""""""""""""""""""""""""""""""""""""""""""""""

The minimizer could fail on a number of systems.

:issue:`2641`

Disallow pull geometry direction-periodic with AWH
""""""""""""""""""""""""""""""""""""""""""""""""""

This could lead to incorrect behavior or a cryptic error message.

:issue:`2923`

Fixed mdrun -nsteps option
""""""""""""""""""""""""""

Fixed that the, deprecated, mdrun option -nsteps only allowed extension
of the simulation under certain conditions.

:issue:`2881`

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

gmx cluster -clndx indices now correct
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

The reported indices of trajectory frames in clusters were
too small by one.

:issue:`2926`

gmx editconf -f in.pdb -o out.pdb again preserves chain IDs
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

This had been inadvertently broken and is now fixed.

:issue:`2900`


Tools again accept .tpr files as input
"""""""""""""""""""""""""""""""""""""""

The pdb2gmx, solvate, and insert-molecules tools could no longer
accept input configurations contained in .tpr format files. This
is now fixed.

:issue:`2900`

Fix segmentation fault when preparing simulated annealing inputs
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

grompp was unable to prepare tpr files for inputs containing simulated annealing
procedures. The code has been fixed to allow the generation of those files again.

:issue:`2871`
       
Fixes that affect portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Fix error in AVX 512 detection code
"""""""""""""""""""""""""""""""""""

The CMake detection code had a typo that could lead to wrong detection results.

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

Added warning with the use of GROMOS force fields
"""""""""""""""""""""""""""""""""""""""""""""""""

grompp now warns when a GROMOS force field is used. The GROMOS force fields
have been parametrized with a physically incorrect multiple-time-stepping
scheme for a twin-range cut-off. When used with a single-range cut-off,
physical properties, such as the density, might be off from the intended values.

:issue:`2884`

Prevented internal build of FFTW with clang and AVX-512 SIMD
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Prevented the internal build of FFTW with clang from attempting to
configure FFTW to compile with AVX-512 support. That SIMD level is not
supported by FFTW with the clang compiler, and compilation fails.

:issue:`2892`

Updated performance guide for recent Intel processors with AVX512 instruction support
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Noted the tradeoffs between CPU frequency and SIMD throughput and advising users to
prefer AVX2 over AVX512 in GPU-offload or highly parallel MPI cases.

Updated release notes for 2019.1
""""""""""""""""""""""""""""""""

A :ref:`fix <release-notes-2019-1-gpu>` made to GPU kernels in 2019.1 was
thought to resolve :issue:`2845` but further investigation suggests that
the real cause is not yet known. 

