Improvements to |Gromacs| tools
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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``gmx msd`` has been migrated to the trajectoryanalysis framework
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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
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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.