Performance improvements#

Improved performance for inhomogeneous systems#

The performance of systems with a lot of empty space is improved by optimizing the pair search grid for the effective atom density.

Issue 4805

Flexible hydrogen mass repartitioning using grompp#

Instead of using pdb2gmx, which modifies the topology, a flexible scheme for hydrogen mass repartitioning is now available in grompp through the mass-repartition-factor mdp option. This provides easy access to a performance improvement of close to a factor two.

Issue 4866

Small performance regression to achieve more accurate pressure#

To lower the effect on Lennard-Jones pair interaction on the pressure, the Verlet buffer has been increased for most simulations using default mdp settings. This can lead to a few percent performance loss, in particular when using GPUs. The effect will be strongest for systems with no or weak electrostatics, which includes most coarse-grained systems.

Issue 4861

Reduced grompp and mdrun setup time for systems with many atom types#

The Verlet buffer calculation could take many minutes for systems with thousands of different Verlet buffer atom types (different atom type and charge). Such times have now been reduced to seconds.

Issue 4892

With wall potentials, bonded interactions can now be run on GPUs#

HeFFTe multi-GPU FFT plan options are now configurable#

New environment variables GMX_HEFFTE_RESHAPE_ALGORITHM, GMX_HEFFTE_USE_GPU_AWARE, GMX_HEFFTE_USE_PENCILS, and GMX_HEFFTE_USE_REORDER permit the HeFFTe plan options to be configured at run time. The performance obtained can vary with the quality of implementation of e.g. the GPU-aware MPI library, as well as the layout and number of the GPUs participating in the 3D-FFT. Users can now find and use the best settings for their case. See the HeFFTe documentation for more details.