GROMACS 2016 Release Notes

These release notes document the functionality changes that have taken place in GROMACS since version 5.1.

Some bug fixes are mentioned here, but those fixed in 5.0 or 5.1 branches are (or will be) documented there. If the same functionality is supported in both branches, bugs fixed on older branches can generally be assumed to be fixed in patch releases of subsequent major/minor versions.


Here’s some highlights of what you can expect, along with more detail in the links below!

  • As always, we’ve got several useful performance improvements, with or without GPUs. CPU-side SIMD and threading enhancements will make GPU-accelerated simulations faster even if we’d left the GPU code alone! Thanks to these and additional GPU kernel improvements, in GPU-accelerated runs expect around 15% improvement in throughput. (And not just for plain vanilla MD, either... the pull code now supports OpenMP threading throughout, and multi-simulations have less coupling between simulations.)
  • We have a new C++11 portability layer permitting us to accelerate in SIMD on the CPU lots of minor routines. These will also often improve runs that use accelerators or many nodes through better load balancing. POWER8, ARM64, AVX512 (KNL), and more are fully SIMD accelerated now because they are supported in the new portability layer!
  • We made further SIMD acceleration of bonded interactions which reduces their calculation time by about a factor of 2. This improves load balance at high parallelization by a factor of 2, and shows significantly better scaling.
  • Similarly, SIMD acceleration of SETTLE reduces the time for constraints by a factor of 3 to 5 - which has a strong effect for GPU runs.
  • OpenCL GPU support is now available with all combinations of MPI, thread-MPI and GPU sharing (ie. the same as CUDA). Kernel performance has improved by up to 60%. AMD GPUs benefit the most, OpenCL on NVIDIA is generally still slow.
  • Tools in the new analysis framework can handle trajectories that are subsets of the simulation system.
  • New pull coordinate geometries angle-axis, dihedral, and normal angle.
  • Checkpoint restarts work only in the cases where the implementation can always do what the user wants.
  • The version numbering has changed to be the year of the release, plus (in future) a patch number. GROMACS 2016 will be the initial release from this branch, then GROMACS 2016.1 will have the set of bugs that have been fixed in GROMACS 2016, etc.