Features removed in this version

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.

Issue 1424

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.

Issue 1137

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 It has been superseded by the Verlet cut-off scheme, and removed before the rest of the group scheme because its implementation made it difficult to address other issues.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.

Issue 1618.