GROMACS 2016.2 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
  • Add grompp check for equipartition violation risk for decoupled modes
  • Disallow overwriting of dihedral type 9
  • Fixed flat-bottom position restraints + DD + OpenMP
  • Fixed multi-domain reruns
• Fixes for mdrun performance issues
  • Corrected CUDA sm_60 performance
• Fixes for gmx tools
  • Fixed some FFT handling in cross-corrrelation calculations
  • Fixed gmx rmsf -q -oq
  • Fixed crash in gmx order
  • Fixed minor trjconv bug
  • Fixed time label print in gmx vanhove
  • Handled issuing warnings correctly in xpm2ps and membed
  • Corrected documentation about eigenvalue handling
  • Made editconf B-factor attachment more useful in practice
  • Fixed possible memory error with long selections
  • Fixed use of position variables with plus/merge
• Improved documentation
  • Made several minor improvements to documentation and messages to users
  • Clarified use of tau-p and pcoupltype
• Portability enhancements
  • Fixed x86 conditional on IBM s390x
• Build system enhancements
  • Fixed compilation with CMAKE_CXX_FLAGS=”-Wall -Werror”
  • Stopped trying to use objdump –reloc in the build system on Mac
  • Improved the support for plugin loading in the build system
  • Turn off hwloc support when static lib found
  • Fixed build with GMX_EXTERNAL_TNG=ON
• House-keeping that reduces users’ problems
  • Mdrun prints invalid performance data less often
  • Added a runtime check for number of threads in bonded code
  • Fixed integer narrowing in TNG reading for long trajectories
  • Fixed logic of TRR reading