GROMACS 2024.4 release notes#
This version was released on TODO, 2024. These release notes document the changes that have taken place in GROMACS since the previous 2024.3 version, to fix known issues. It also incorporates all fixes made in version 2023.6 and earlier, which you can find described in the Release notes.
Fixes where mdrun could behave incorrectly#
Fix missing non-bonded interactions close to cut-off with GPUs#
The GPU rolling pruning employed with the dual pair list setup used
an incorrect list part calculation. This caused a few parlist entries
not to be updated after the initial pruning, leading to a small number
of missing pair interactions. Unless the pair list lifetime nstlist
was very large, these interactions were close to the cut-off and therefore
the errors were small.
Affected simulations: all GPU accelerated runs using GROMACS versions
starting with the 2018 release with dual pair list enabled.
This is enabled automatically with default Verlet buffering, but
it is disabled if the Verlet buffer is manually set
(or if the GMX_DISABLE_DYNAMICPRUNING environment variable is set).
Impact: Our analysis shows that the error caused by the missing interactions
does not have a measurable effect on either forces or energy conservation
in most atomistic simulations with default simulation settings.
While a manually increased nstlist, hence increased (outer) pair list lifetime,
leads to an increase in the number of missing interactions, for useful value of
nstlist the effect is still negligible.
There can be measurable effects in systems with vacuum, gas, or with
excessively large nstlist values. In our testing we could not detect artifacts
apart from systems crashing, so the chance of undetected incorrect results is small.
Fix Colvars output files always written to the working directory.#
Colvars output files are now written in the same folder as edr file.
Forbid the usage of triangle constraints with -update gpu#
Prevent using update on GPU if there are triangle constraints.
Fixes for gmx tools#
Fix dump crash with Colvars values#
Fix gmx dump crash when trying to output the binary Colvars state file.
Fixes that affect portability#
Miscellaneous#
Fix various crashes when GMX_USE_COLVARS=NONE#
Colvars MDModule did not defined the Colvars custom mdp variables when the Colvars library was not compiled, preventing tools read correctly a tpr file generated with a GROMACS-Colvars version. Prevent also the creation of a tpr file if Colvars module is activated whereas GROMACS was not compiled with Colvars. Proper exit if a Colvars simulation is launched whereas GROMACS was not compiled with Colvars.
Fix reading cgroups in some kubernetes containers#
Modern versions of kubernetes/docker do not appear to mount /etc/mtab in the containers, and if we did not find cgroups we would not detect CPU limits set through cgroups. Fixed by reading /proc/mounts instead. This will only influence performance when running in (some) containers.