GROMACS 2025.3 release notes¶

This version was released on August 29th, 2025. These release notes document the changes that have taken place in GROMACS since the previous 2025.2 version, to fix known issues. It also incorporates all fixes made in version 2024.6 and earlier, which you can find described in the Release notes.

Fixes where mdrun could behave incorrectly¶

AWH for free-energy lambda coordinate was not active¶

When using AWH for a free-energy lambda coordinate (and no other dimension), the lambda state would remain at the initial state and all resulting free energies would be zero. Affected versions: 2024.4, 2024.5, 2025.0, 2025.1 and 2025.2.

Issue 5371

`gmx mdrun` now throws with input inconsistent with the modular simulator¶

By default, gmx mdrun can choose the modular simulator if possible and fall back on the legacy simulator if needed. The behaviour can be specified with the use of documented environment variables. After this fix, the use of GMX_USE_MODULAR_SIMULATOR environment variable is properly honored. If the simulation cannot use the modular simulator, an error is given.

Issue 5339

Fixes for `gmx` tools¶

Fixes that affect portability¶

SYCL build now works with BUILD_SHARED_LIBS=off¶

Previously gmx and some test binaries failed to link to libgromacs.a because the required information to link to the SYCL runtime library is missing in that case. Linking of executables in SYCL builds is now more robust.

Issue 5341

Fix build with ROCm 7 and newer¶

Building and linking GROMACS would fail due to changes in the linking behaviour of the main HIP library.

Issue 5380

Building GROMACS would fail due to __AMDGCN_WAVEFRONT_SIZE macro removal in ROCm 7.

Issue 5259

Improved configuration error message with SYCL and VkFFT¶

Configuring GROMACS with SYCL and VkFFT, targeting Intel devices, would result in an error meessage implying using VkFFT with SYCL wasn’t suported at all. The message is now clarified to include the statement that this lack of support only applies to Intel devices.

Issue 5401

Fix detection of unusable MKL GPU offloading library during configuration¶

Configuration would previously happily proceed even if development headers of MKL GPU offloading library were not found, causing the compilation to fail. This now results in an error.

Issue 5400

Fix build for NVIDIA sm_101 / sm_110 devices¶

Issue 5366

Miscellaneous¶

Documented that PME tuning in multi-replica simulations can give suprising results¶

PME tuning chooses between nominally equivalent model physics, yet there is no guarantee of consistency between (say) the tunings chosen for different replicas in a multi-replica simulation, so the fine details of comparisons of potential energy can be surprising. Disabling PME tuning for e.g. testing Hamiltonian replica-exchange simulations with PLUMED is advised.

Issue 5278

mdrun reported double the number of domain decompositions when using GPUs¶

When using GPUs, the cycle count table at the end of the log file reported a number of calls for Domain decomp. that was too high by a factor of one plus the number of dimensions that were decomposed. The times and cycle counts were correct.

Issue 5369

Support added for compilation with NVIDIA CUDA 13 toolkit¶

Addition of a compilation option necessary to avoid CUDA build failures when using the NVCC compiler from version 13 of the CUDA toolkit.

Issue 5389

Avoid installing 3rd party header files¶

Fixed a regression where GROMACS installed muParser headers, causing conflicts with the separate muParser package if installed.

Issue 5282

libgromacs now only links to MPI libraries when explicitly required¶

Formerly gmxapi could have erroneously triggered GROMACS to compile and link with an MPI library. This is now fixed.

Issue 5395

Declared gmxapi option before finding MPI package¶

Formerly gmxapi was set up after MPI libraries, which caused a subsequent run of CMake to decide to find MPI libraries to help gmxapi even when libgromacs didn’t need those libraries. Now the CMake cache does not vary between successive runs in this way.