Features removed in this version¶
Removed temporary symlinks from pre-5.0 tool names¶
GROMACS 5.0 provided symlinks from the old-style g_tool to new-style
gmx tool as a convenience to users during the transition period.
That period is now over, so gmx tool (or gmx_mpi tool) is the
only way to use GROMACS in 5.1. The mdrun-only build will build
mdrun (or mdrun_mpi as appropriate).
Removed support for partial matches for selection keywords¶
he selection parser tried to be nice to the user and also accept unambiguous prefixes of keywords, but this also has a lot of side effects that can be confusing (e.g., it was impossible to create variables that had names that were prefixes to keywords or to other variable names). There are still a few synonyms for keywords where there is a natural abbreviation.
Removed mdrun -testverlet¶
This was only intended for quick performance testing of old .tpr files
during the transition period. The window where that was useful has
passed. There is no need to
preserve this until the formal removal of the group scheme.
Removed iteration + constraints framework¶
Getting rid of iteration + constraints required by the use of MTTK + constraints, in order to simplify the main MD loop.
Implemented mdrun check so that an old .tpr with MTTK + any form of constraints cannot be run.
Removed heuristic group-scheme neighbour-list updates¶
Formerly, -1 == nstlist would trigger the use of an algorithm that did
neighbour searching only when particles had moved far enough that
there might be a need to update the list. This supported obtaining
better energy conservation with the group cut-off scheme. It has been
superseded by the Verlet cut-off scheme, and removed before the
rest of the group scheme because its implementation made it
difficult to address other issues.
Removed mdrun -seppot¶
This output of rank-local energies is not needed for any routine use, and isn’t much use in mdrun -debug either. Removing it simplifies a few code paths, including removing some dependencies on writing sane things to the log file.
Removed support for .tpa, .tpb, .tpx, .trj file formats¶
These haven’t been useful for years
Removed gmx protonate tool¶
This tool appears to have been largely unused, since testing shows it crashes for a normal trajectory all the way back to GROMACS 4.6. It might reappear in the future if there is demand.