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.
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.