Deprecated functionality¶
Changes anticipated to GROMACS 2024 functionality¶
The analysis tool gmx chi no longer deprecated¶
Given the community interest, the decision was made to keep gmx chi.
Functionality deprecated in GROMACS 2024¶
The analysis tool gmx gyrate-legacy deprecated¶
gmx gyrate has been partly re-implemented in the modern GROMACS analysis framework.
The old implementation is still available as gmx gyrate-legacy. Please plan to update to the new version.
Please let the GROMACS developers know of desired functionality missing from, or broken in, the new implementation.
The analysis tool gmx hbond-legacy deprecated¶
gmx hbond has been partly re-implemented in the modern GROMACS analysis framework.
The old implementation is still available as gmx hbond-legacy. Please plan to update to the new version.
Please let the GROMACS developers know of desired functionality missing from, or broken in, the new implementation.
The analysis tools gmx sans and gmx saxs deprecated¶
gmx sans and gmx saxs has been partly re-implemented under new name gmx scattering in the modern GROMACS analysis framework.
The old implementations are still available as gmx sans-legacy and gmx saxs-legacy. Please plan to update to the new version.
Please let the GROMACS developers know of desired functionality missing from, or broken in, the new implementation.
The Xeon Phi support will be removed¶
Intel Xeon Phi series of accelerators has been discontinued in 2020, and most supercomputers using it are now retired. The support for Xeon Phi is deprecated in GROMACS 2024 and will be removed in the next release.
Functionality deprecated in GROMACS 2022¶
GMX_OPENCL_NB_CLUSTER_SIZE CMake variable deprecated in favor of GMX_GPU_NB_CLUSTER_SIZE¶
Both OpenCL and SYCL support different cluster sizes, so GMX_GPU_NB_CLUSTER_SIZE should be used going forward.
Guessing masses and atomic radii from atom names is deprecated¶
When atom masses or van-der-Waals radii are needed, we suggest building a proper GROMACS topology instead of using PDB files directly, even if the tool supports it.
Functionality deprecated in GROMACS 2021¶
mdrun -deffnm to be removed¶
This functionality is convenient when running very simple simulations,
because it permits grouping of a set of files that then differ only
their suffix. However, it does not work in the wider case of an
mdrun module (or modules) writing multiple .xvg output
files. The resulting filenames collide. That, and its interaction with
checkpointing and appending, have led to quite a few bug reports.
Because users can use a folder to group files (a standard mechanism
that they understand from experience outside of GROMACS), we can
build and test better software for them if we remove the erstwhile
convenience of mdrun -deffnm. Please update your workflows
accordingly.
OpenCL to be removed as a GPU framework¶
Issue 3818 Work is underway for ports to AMD and Intel GPUs, and it is likely that those ports will not be based on the current GROMACS OpenCL port. Nvidia GPUs are targeted by the CUDA port, and no changes are expected there. The core team can’t maintain, test, and extend up to 4 ports with current resource levels. Since there are no prospects of an emerging GPU vendor in HPC needing OpenCL support, we will remove the OpenCL port once AMD and Intel support is established in other ways.
Support for version 1 of the hardware locality library hwloc¶
Issue 3818 Version 2 has been supported in GROMACS for several
years. The capabilities of newer hardware and hardware-support APIs
are of most interest for GROMACS moving forward, so we should
minimize our testing work and encourage clusters to upgrade older
hwloc installations.
Legacy API¶
Issue 3818 The legacy installed headers have been deprecated for a
while, however we wish to state more broadly that all headers found
within the src directory tree of GROMACS are intended for
internal consumption only, and are thus subject to change without
notice. Further, the form and contents of the libgromacs library
and related CMake targets may change as we move towards building APIs
and supporting machinery that can be stable and supported in the long
term.
Functionality deprecated in GROMACS 2019¶
Generation of virtual sites to replace aromatic rings in standard residues¶
Issue 3254 These are thought to produce artefacts under some circumstances (unpublished results), were never well tested, are not widely used, and we need to simplify pdb2gmx.
Benchmarking options only available with gmx benchmark¶
Issue 3255 Options such as -confout, -resethway, -resetstep are not
intended for use by regular mdrun users, so making them only available
with a dedicated tool is more clear. Also, this permits us to customize
defaults for e.g. writing files at the end of a simulation part in ways
that suit the respective mdrun and benchmark use cases, so -confout
will no longer be required.
gmx mdrun -nsteps¶
Issue 3256 The number of simulation steps described by the .tpr file can be
changed with gmx convert-tpr, or altered in .mdp file before the
call to gmx grompp. The convenience of this mdrun option was
outweighed by the doubtful quality of its implementation, no clear
record in the log file, and lack of maintenance.