Improvements to GROMACS tools

gmx msd has been migrated to the trajectoryanalysis framework

The tool now uses the GROMACS selection syntax. Rather than piping selections via stdin, selections are now made using the “-sel” option.

This migration comes with about a 20% speedup in execution time.

TODO: Modify/Delete this segment as features are added back in. Some rarely used features have yet to be migrated, including:

• Mass weighting of MSDs cannot currently be turned on or off. It is set to on when -mol is set, otherwise off.

• The -tensor option is not yet implemented.

• System COM removal with -rmcomm has not yet been implemented.

• B-factor writing using the -pdb option is not yet supported.

Issue 2368

gmx chi no longer needs residuetypes.dat entries for custom residues

The need to add the names of custom residues to residuetypes.dat has been removed, because it served no purpose. This makes gmx chi easier to use.