GROMACS 2024.4 release notes#

This version was released on October 31st, 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 2023.5 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.

Issue 5138

Add effect of perturbed masses to foreign Hamiltonian differences#

The effect of perturbed masses was missing from the foreign Hamiltonian differences. This meant that effects of perturbed masses were ignored by gmx bar. Note that perturbed masses did contribute to dH/dlambda.

Issue 5195

Fix illegal memory access with more VCM than T-coupling groups#

When there were more center of mass motion removal groups than temperature coupling groups, mdrun could crash due to illegal memory access. This bug did not affect the simulation results.

Issue 5167

Fix crashes when some atoms are not part of a VCM group#

Uninitialized memory was read when some atoms were not part of a center of mass motion removal group. Often this memory contained zero and everything would work as it should. But when this memory was not zero, the simulation would crash within a few steps.

Issue 5181

Fix parameter handling for coarse-grained bonded potentials#

Free-energy perturbation has never been supported for restraint angle, restraint dihedral, and combined bending-torsion potentials sometimes used in coarse-grained force fields. This led to the hypothetical B-state parameters being incorrectly handled in gmx grompp and then incorrectly serialized to/from the .tpr file.

This was generally benign, even when such functional forms were in use. However, when other interactions were perturbed, the incorrect parameter handling made it look like the interactions with wrongly implemented parameters were intended to be perturbed. This condition was sometimes achieved when using alchemical-embedding system-preparation workflows.

Now the hypothetical B-state parameters are handled correctly, so FEP-based workflows can succeed. Perturbation of the above-mentioned interaction types is still not supported, however.

Issue 5129 Issue 5144 Issue 5147

Fix Colvars output files always written to the working directory.#

Colvars output files are now written in the same folder as edr file.

Issue 5122

Forbid the usage of triangle constraints with -update gpu#

Prevent using update on GPU if there are triangle constraints.

Issue 5123

gmx_mpi mdrun could hang when using GPUs and separate PME ranks#

A logic error in task assignment for -nb gpu -pme cpu and separate PME ranks made the (default) -ddorder interleave hang. Now it works.

Issue 4345

Dynamic load balancing was ineffective when special forces were present#

The timing for DLB included the calculation of special forces, e.g. pull code and rotation. As these require communication, imbalance might not have been measured. Now special forces are excluded from the timings.

Issue 5188

Fix incorrect memory access with perturbed non-bonded and OpenMP#

Old, invalid indices could be flagged for reduction of force buffers over OpenMP threads for perturbed non-bonded interactions. This could never lead to incorrect results or crashes. But performance might be improved now.

Issue 5220

Fixes for gmx tools#

grompp checked incorrect B-state charges with free-energy decoupling#

When the couple-moltype options was used, gmx grompp would check the A-state charges instead of the B-state charges. This would lead to incorrect or no warnings when B-state of the system had non-zero net charge.

Issue 5200

grompp, and mdrun, could exit with large mass differences#

When masses of atoms differed more than a factor 327, both gmx grompp and gmx mdrun could exit with an assertion failure about an infinite enery drift estimate.

Issue 5222

Fix dump crash with Colvars values#

Fix gmx dump crash when trying to output the binary Colvars state file.

Issue 5034

Fix element and atom number deduction in during preprocessing#

Two-letter atom names like BR or CL were not correctly handled in the preprocessing during gmx editconf, gmx pdb2gmx and gmx grompp, leading to incorrect element and atom number assignment. This could lead to incorrect element names in output files and possibly incorrect behaviour in QMMM simulations.

Issue 5182

Fix hang observed with NVSHMEM enabled PME-PP force transfers#

A hang in PME-PP force transfers during NVSHMEM runs was resolved, occurring in certain conditions. It should also be noted that the NVSHMEM enabled PME-PP force transfers does not support charge perturbation.

Issue 5136

Fixes that affect portability#

Fix physical validation with Pymbar version 4#

Pymbar version 4 has a different API compared to version 3. Now we support using either of those versions and internally handle the API differences.

Issue 5130

Fix compatibility with VkFFT 1.3.5#

Fix crash on GROMACS shutdown when external VkFFT 1.3.5 is used.

Issue 5184

Miscellaneous#

Work around FetchContent warnings in CMake 3.30 and newer#

CMake 3.30 began to complain about GROMACS use of FetchContent, so now we tell such new versions to use the old policy.

Issue 5140

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.

Issue 5055

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.

Issue 5148

Collected fixes in the Colvars library#

Several bugs, both recent and long-standing, have recently been fixed in the Colvars library: in the list below, the links corresponds to issues or pull request in the Colvars repository.

  • Fixed undefined behavior when getting the current working directory from std::filesystem, which could have affected multiple-walkers metadynamics runs (Colvars PR 728).

  • Fixed the gradients and the metric functions of collective variables of distanceDir type (Colvars PR 724).

  • Fixed the definition of an orientation type collective variable in a rotated frame of reference (Colvars PR 715).

  • Implemented the contribution of fitting to the forces applied onto of variables with vector values defined in a rotated fram (Colvars PR 713).

  • Fixed a crash in certain metadynamics simulations without using interpolating grids (Colvars PR 706).

  • More consistent behavior when defining multiple biases and running with more than one thread per task (Colvars PR 694).

  • Prevented the creation of spurious output files for runtime histograms (Colvars PR 675).

Enable NVCC flags checks for Windows#

When building GROMACS for Windows with CUDA support, the checks for testing compatible compute architectures were disabled. Hence, GROMACS was trying to compile for all of them which can induced failed builds when CUDA is not compatible anymore with old compute architectures.

Issue 5152