GROMACS 2016.3 Release Notes

These release notes document the changes that have taken place in GROMACS since the initial version 2016 and subsequent patch releases, to fix known issues. It also incorporates all fixes made in version 5.1.4 and several since.

• Fixes where mdrun could behave incorrectly
  • Fixed mdrun with separate PME ranks hanging upon exit
  • Fixed handling of previous virials with md-vv integrator
  • Fixed an incorrect check that nstlog != 0 for expanded ensembles
• Fixes for gmx tools
  • Fixed gmx tune_pme detection of GPU support
  • Fixed spacing in gmx tune_pme call to thread-MPI mdrun
  • Fixed minor issues in gmx traj -av -af
  • Removed rogue printing to xvg file in gmx mindist
  • Fixed bug in gmx solvate -shell if it yielded 0 SOL.
  • Corrected output of gmx do_dssp -sc
• Improved documentation
  • Made several minor improvements to documentation and messages to users
  • Documented that we now support AMD GCN on Mesa/LLVM
  • Documented running Clang static analyzer manually
• Portability enhancements
  • Enabled avx512 in the GROMACS FFTW build only if the compiler supports it
  • Worked around false positives in SIMD test from bug in xlc 13.1.5
  • Fixed compile with icc of GMX_SIMD=None