GROMACS 5.1.2 Release Notes

These release notes document the changes that have taken place in GROMACS since version 5.1.1 to fix known issues.

• Fixes where mdrun could return incorrect results
  • Fixed LINCS triangle constraint thread issue
  • Corrected LINCS dHdl contribution
  • Fixed SETTLE error handling
  • Fixed exact continuation from non-energy steps
  • Fixed energy file continuation with md-vv
  • Fixed energy average with continuation
  • Backported some md-vv fixes
  • Required Nose-Hoover with MTTK
  • Fixed Trotter integration
  • Stopped global communication depending on integrator
  • Fixed dEkin/dl handling with multiple ranks
  • Fixed TPI ignoring PME mesh contributions.
  • Fixed an error in multi-sim communication
  • Fixed a bug with pull group weights
  • Removed mdrun fatal_error with P3M-AD
  • Fix mdrun removing Verlet buffer with EM
• Fixes for mdrun performance issues
  • Restored a lost performance tweak with AdResS
  • Fixed walltime measurement with bgclang
  • Fixed PME load balancing skipping a setup
  • Brought performance estimation up to date
• Fixes for gmx tools
  • Corrected vector check in gmx check
  • Fixed -npstring command line argument in gmx tune_pme
  • Made gmx tune_pme work with -cpi -deffnm combination
• New consistency checks
  • Added check for double perturbation
  • Fix grompp not warning when .mdp values have wrong types
• Build system enhancements
  • Allowed NVML support to be toggled
• Improved documentation
  • Updated pair-list buffer description in reference manual
  • Rotated Figure 8.2 in manual
  • Added suggestions to install guide and cmake for updating binutils
  • Fixed a duplicate LaTeX equation label in the reference manual
  • Documented how potential-switch works
  • Updated references to HTML and online documentation
  • Documented limitations on 32-bit Linux
  • Improved documentation on OpenCL issue with NVIDIA
• House-keeping that reduces users’problems
  • Avoided finding C++ bindings for SGI’s MPT
  • Stopped using UNDEFINED as name of a symbol
  • Fixed some OpenCL issues