Removed functionality#

Group cut-off scheme#

The group cut-off scheme has been removed. Several kinds of simulation that depend on it no longer work.

  • Simulations under vacuum conditions are not supported.

  • User supplied tables for short-range nonbonded interactions are not supported.

  • Switched short-range nonbonded interactions with PME are not supported.

  • Membrane embedding is deactivated.

  • QMMM is not supported.

Issue 1852

Generalized reaction-field#

This only worked correctly with the group scheme. Note that generalized reaction-field simulations can still be performed using standard reaction field and computing the dielectric constant manually.

gmx anadock#

The gmx anadock tool was removed since it does not belong in gromacs (it analyzes AutoDock outputs).

gmx dyndom#

The gmx dyndom tool was removed since it does not belong in gromacs (it analyzes DynDom outputs).

gmx morph#

The gmx morph tool was removed since it yields non-physical structures that can easily be done by a script.

gmx mdrun -gcom#

This feature sometimes overrode the effects of various .mdp settings in a way that was difficult to understand and report. A user who wants to do communication between PP ranks less often should choose their nst* mdp options accordingly.