Changes anticipated to GROMACS 2020 functionality

Functionality deprecated in GROMACS 2020

Support for 32bit architectures

There are no current or planned large scale resources using 32bit architectures, and we have no ability to properly test and evaluate them.

Free-energy soft-core power 48

Free-energy soft-core power 48 is almost never used and is therefore deprecated.

Functionality deprecated in GROMACS 2019

Generation of virtual sites to replace aromatic rings in standard residues

These are thought to produce artefacts under some circumstances (unpublished results), were never well tested, are not widely used, and we need to simplify pdb2gmx.

Benchmarking options only available with gmx benchmark

Options such as -confout, -resethway, -resetstep are not intended for use by regular mdrun users, so making them only available with a dedicated tool is more clear. Also, this permits us to customize defaults for e.g. writing files at the end of a simulation part in ways that suit the respective mdrun and benchmark use cases, so -confout will no longer be required.

gmx mdrun -nsteps

The number of simulation steps described by the .tpr file can be changed with gmx convert-tpr, or altered in .mdp file before the call to gmx grompp. The convenience of this mdrun option was outweighted by the doubtful quality of its implementation, no clear record in the log file, and lack of maintenance.