GROMACS 2020.1 release notes
----------------------------

This version was released on March 3rd, 2020. These release notes
document the changes that have taken place in GROMACS since the
previous 2020 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 GitLab, without the
   a space between the colon and number!

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

Fix fatal error with mdrun -multidir with more than 1 rank per simulation
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

:issue:`3296`

Fix deadlock in mdrun runs with multiple ranks and separate PME ranks
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When multiple PP ranks as well as separate PME ranks are used, mdrun could
deadlock before starting the PP-PME balancing.

:issue:`3335`

Avoid mdrun assertion failure when running with shells and update on a GPU
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

A check for shells has been added in the mdrun task assignment code,
so that mdrun falls back to CPU or produces a clear error message
when attempting to run with shells and update on a GPU.

:issue:`3303`

Allow large prime factors in the mdrun MPI rank count
"""""""""""""""""""""""""""""""""""""""""""""""""""""

The domain decomposition would refuse to run with large prime factors
in the MPI rank count even when the grid was specified by the user.

:issue:`3336`

Actually fix PME forces with FE without perturbed q/LJ
""""""""""""""""""""""""""""""""""""""""""""""""""""""

PME would incorrectly ignore the mesh forces on perturbed atoms when
no charges or LJ atom types were actually perturbed. Note that this
is a rather uncommon scenario.

:issue:`2640`
:issue:`3359`

Avoid deadlock when checking for missing DD interactions
""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When missing bonded interactions after domain decomposition were detected,
mdrun was deadlocking instead of exiting with a failure.

:issue:`3373`

Fix checkpoint restarts using Parrinello-Rahman and md-vv
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Checkpoints using Parrinello-Rahman and md-vv (only implemented in
the new modular simulator approach) could not be read.

:issue:`3377`

Avoid overzealous program abort with orientation restraints
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

It could happen that mdrun would abort on checking orientation restraints in multiple
molecules even though no restraints where applied to them.

:issue:`3375`

Add fatal error for mdrun -multidir when simulations sharing state start at different step
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When (re)starting mdrun -multidir for simulations sharing state data
(e.g., replica exchange, AWH with bias sharing or NMR ensemble averaging)
having a different initial step only caused a note to be printed, which
could lead to simulations getting out of sync. Now a fatal error is issued
in this situation.

:issue:`2440`
:issue:`3990`

Correct skewed box using modular simulator without DD
"""""""""""""""""""""""""""""""""""""""""""""""""""""

Using modular simulator without DD, it was not checked whether the box
was getting overly skewed when using pressure control.

:issue:`3383`

Fix NMR restraints using modular simulator
""""""""""""""""""""""""""""""""""""""""""

Using NMR restraints (distance or orientation restraints) under modular simulator
did not work as expected. All orientation restraint simulations would fail with a
segmentation fault, as would distance restraint simulations using time averaging.
All other distance restraint simulations would run correctly, but output to the
energy trajectory would only occur if it coincided with general energy writing
steps.

:issue:`3388`

Avoid integer overflow when using dispersion correction
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

A change in the integer type storing the index meant that the value could overflow
and turn negative, leading to wrong lookup and unphysical values.

:issue:`3391`

Fix too small pairlist buffer on Intel GPUs
"""""""""""""""""""""""""""""""""""""""""""

The pairlist buffer generated for Intel GPUs was slightly too small,
because it assumed a 4x4 atom-cluster pair kernel instead of 4x2.

:issue:`3407`

Fix checkpoint files getting out of sync with simulations sharing data
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

When simulations share data, e.g., replica exchange, AWH with bias sharing
or NMR ensemble averaging, MPI barrier have now been added before renaming
the checkpointing files to avoid that checkpoints files from the simulations
can get out of sync. Now in very unlikely cases some checkpoint files might
have temporary names, but all content will be in sync.

:issue:`2440`

Fix simulations using graph and modular simulations
"""""""""""""""""""""""""""""""""""""""""""""""""""

Simulations using modular simulator and a graph object would fail with a
segmentation fault.

:issue:`3389`

Fix center of mass motion removal with frozen atoms
"""""""""""""""""""""""""""""""""""""""""""""""""""

When frozen atoms were part of center of mass motion removal groups,
they would still contribute to the mass of those groups. This meant that
the COM velocity correction was (slightly) too small. Now completely
frozen atoms are removed from COM removal groups by grompp.
When atoms are only frozen along one or two dimensions and part of
a COM removal group, grompp now issues a warning.

:issue:`2553`

Fix temperature calculation when center of mass motion is removed for part of the system
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

In the uncommon case where the center of mass motion is removed for part of the system
but not the whole system, the number of degrees of freedom for the part without
COMM removal would be incorrectly lowered by 3.

:issue:`3406`

Fix possible issue with picking undefined NB kernel types
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""

The CPU reference implementations for the NB kernels were missing some definitions for specific kernel
types. This only affected installations that have SIMD explicitly turned off, something that is
unlikely to happen in production environments.

:issue:`2728`

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

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

Add support for ICC NextGen
"""""""""""""""""""""""""""

Add support for Intel Compiler based on LLVM technology.
To compile GROMACS with this compiler use ``CXX=icpc CXXFLAGS=-qnextgen cmake``.

Document known issues with OpenCL on Volta and Turing
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

:issue:`3125`

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

Fix check for modified source files in release tarballs
"""""""""""""""""""""""""""""""""""""""""""""""""""""""
It could happen that modifications to the source tree were not picked
up if they happened after the build directory had been generated.

:issue:`3302`

