GROMACS 2024.3 release notes#
This version was released on TODO, 2024. These release notes document the changes that have taken place in GROMACS since the previous 2024.2 version, to fix known issues. It also incorporates all fixes made in version 2023.5 and earlier, which you can find described in the Release notes.
Fixes where mdrun could behave incorrectly#
Remove double dispersion correction with MTTK barostat#
When the MTTK barostat was used with dispersion correction, the pressure correction was applied twice. This caused the density to be too high.
Correct zero Verlet buffer for system with only large masses#
For system with most masses much larger than zero, the Verlet buffer estimate could be zero. Coarse-grained simulations could be affected by this issue.
Fix incorrect energy group pair assignment of pair interactions#
Energies for bonded pair interactions, typically 1-4 interactions, would be assigned to incorrect energy group pairs. With free-energy calculations this could lead to illegal memory access.
mdrun now computes the initial bonded distancs with periodic molecules#
When using periodic molecules, mdrun could quit with an error message about multiple assignments of bonded interactions telling the user to report the issue. The actual source of this was that mdrun did not determine the communication distance required for bonded interactions. Now this distance is determined.
Avoid using invalid device streams#
Issue has only been seen via assertions in the GCC 13 standard library that guard against null-pointer dereferences. The dereferenced null pointers were never used in actual simulations.
Fixes for gmx tools#
Permit gmx tune_pme to understand md.log files#
The format of md.log files changed in 2024 which broke the ability of
gmx tune_pme to understand how previous runs worked by parsing that
file. Now gmx tune_pme understands better.
Avoid crash of convert-tpr on velocity-less tpr files#
The convert-tpr now works on tpr files that do not contain velocities, as generated for, e.g., energy minimization.
Avoid premature termination when using gmx hbond#
Fixed an error that caused gmx hbond to prematurely terminate if there were no donors or acceptors of hydrogen bonds in the chosen selection.
Add grompp warning about zero AWH cover diameter when sharing a bias#
Fix TPR generation with Andersen Massive thermostat and constraints#
A restriction to not generate TPR files for the Andersen thermostat with constraints was incorrectly applied to also the Andersen Massive thermostat.
Fixed filenames of generated CP2K files in QMMM MdModule#
If there were no files provided with grompp -qmi option, module used topol/_cp2k.inp instead of topol_cp2k.inp