- Update to 2024
* Highlights:
- The Colvars library can now be used natively from GROMACS. This
simplifies the use of advanced enhanced sampling simulations.
- Reduced artifacts from Lennard-Jones pair interactions on the
pressure by a configurable increase of the Verlet buffer. Can
lead to a slight performance loss, especially for coarse-grained
systems.
- Corrected several aspects of the deform option. Now simulations with
box deformation behave correctly under high shear or when a solid or
membrane fractures. This also means that the deform option is now
suitable for computing viscosities.
- New option for hydrogen mass repartitioning in grompp enables easy
access to performance improvements.
- Improvements to AWH, such as better control of the histogram growth
factor as well as enabling automatic scaling of the target distribution
based on the AWH friction metric.
- Configurable HeFFTe multi-GPU FFT options lets users fine-tune the
settings for specific use-cases.
* See https://manual.gromacs.org/2024.0/release-notes/index.html
OBS-URL: https://build.opensuse.org/request/show/1143398
OBS-URL: https://build.opensuse.org/package/show/science/gromacs?expand=0&rev=35
- Update to 2023
* Highlights:
- The SYCL GPU implementation, which is the GPU portability
layer that supports all major GPU platforms, has received
major extensions in support for both platforms and features.
To ensure portability in practice, the GROMACS GPU portability
layer is actively developed with multiple SYCL implementations
(hipSYCL, oneAPI DPC++, IntelLLVM) and regularly tested on
multiple GPU backends.
- SYCL supports more GPU offload features: bonded forces and
direct GPU-GPU communication with GPU-aware MPI.
- SYCL hardware support includes AMD (including RDNA support
added here) and Intel for production as well as NVIDIA GPUs
(not for production).
- SYCL optimizations targeting important HPC platforms.
- PME decomposition has been optimized and extended to support
offloading the entire PME calculation to multiple GPUs,
including the FFT computation; when combined with cuFFTmp or
heFFTe this enables much improved strong scaling
(experimental feature).
- CUDA Graph support has been added to execute GPU-resident
single-/multi-GPU simulations using thread-MPI entirely on the
GPU to improve performance (experimental feature).
- New ensemble temperature mdp options allow setting the
temperature of the ensemble for simulations without
temperature coupling or with different reference temperatures.
- With gmx dssp, GROMACS now has a native implementation of the
DSSP algorithm, which replaces gmx do_dssp.
* See https://manual.gromacs.org/2023/release-notes/index.html
- Update to 2022.6
* Bugfix release, see
https://manual.gromacs.org/2023/release-notes/2022/2022.6.html
- Update to 2022.5
* Bugfix release, see
https://manual.gromacs.org/2023/release-notes/2022/2022.5.html
OBS-URL: https://build.opensuse.org/request/show/1077078
OBS-URL: https://build.opensuse.org/package/show/science/gromacs?expand=0&rev=33
- Update to 2022.3
* Bugfix release, see
https://manual.gromacs.org/current/release-notes/2022/2022.3.html
- Update to 2022.2
* Bugfix release, see
https://manual.gromacs.org/current/release-notes/2022/2022.2.html
- Update to 2022.1
* Highlights:
- Free-energy kernels are accelerated using SIMD, which make
free-energy calculations up to three times as fast when using GPUs
- A new formulation of the soft-cored non-bonded interactions for
free-energy calculations allows for a finer control of the alchemical
transformation pathways
- New transformation pull coordinate allows arbitrary mathematical
transformations of one of more other pull coordinates
- New interface for multi-scale Quantum Mechanics / Molecular
Mechanics (QM/MM) simulations with the CP2K quantum chemistry package,
supporting periodic boundary conditions.
- grompp performance improvements
- Cool quotes music playlist
- Additional features were ported to modular simulator
- Added AMD GPU support with SYCL via hipSYCL
- More GPU offload features supported with SYCL (PME, GPU update).
- Improved parallelization with GPU-accelerated runs using CUDA and
extended GPU direct communication to support multi-node simulation
using CUDA-aware MPI.
* See https://manual.gromacs.org/current/release-notes/2022/2022.1.html
- split off libmuparser2 into separate package
OBS-URL: https://build.opensuse.org/request/show/1011218
OBS-URL: https://build.opensuse.org/package/show/science/gromacs?expand=0&rev=22
- Update to version 2021.2.
- Turn SKIP_RPATH=OFF and SKIP_INSTALL_RPATH=ON instead; skipping rpath use entirely causes linking issues with tests, but we still want to disable rpaths for the installed libs of course.
- Rename %{name}-bash to %{name}-bash-completion in keeping with naming convention followed by other packages.
- Add lapack-devel to BuildRequires to use system versions of blas and lapack.
- CMake 3.13 or higher is required; adapt BuildRequires accordingly.
- Disable testing for i586: doesn't work with gmock.
- Adapt to updated cmake options and drop no longer applicable ones.
OBS-URL: https://build.opensuse.org/request/show/902897
OBS-URL: https://build.opensuse.org/package/show/science/gromacs?expand=0&rev=10
- version bump to 2019.5 details here:
http://manual.gromacs.org/documentation/2019.5/release-notes/2019/2019.5.html
Hightlights:
- Fix use of uninitialized data on PME only ranks
- Fix out of range memory access with free-energy calculations
- Fix error with intermolecular interactions and domain decomposition
- Fix issues with AWH with pull-geometry ‘direction’ to be periodic
- Remove assertion failure with AWH when not using the initial stage
- Fix dihedral angle calculation near 180 degree boundary
- Remove problematic output of gmx angle tool
- Check that libhwloc headers and runtime match
- Fix .gro file formatting with large boxes
- Fix duplicate PDB CONECT record output
OBS-URL: https://build.opensuse.org/request/show/759038
OBS-URL: https://build.opensuse.org/package/show/science/gromacs?expand=0&rev=4
