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. There is a new option called ``-maxtau``,
which limits maximum time delta between frames to compare for calculating MSDs. This will allow
users who otherwise would run into out-of-memory errors and slow execution with large systems
to restrict sampling to useful tau values.

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

Some rarely used features have yet to be migrated, including:

- 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.

A slight behavior change is the removal of the -mw option. ``gmx msd`` with ``-mol`` will
take the MSD of the center-of-mass of of molecules, while no mass-weighting is done
when ``-mol`` is not selected. In previous |Gromacs| versions, ``-mw`` was on by default,
and ``-nomw`` was silently ignored when ``-mol`` was chosen. This change will only cause
different results when performing MSD calculations on a non-homogenous group of particles without
``-mol`` set.

: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.

``gmx wham`` has had minor improvements to its text output
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Reporting about file handling and input-file column contents are easier to
follow.

``gmx do_dssp`` supports DSSP version 4
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The newer DSSP version 4 program can be used by ``do_dssp`` by specifying 
option ``-ver 4`` and setting the DSSP environement variable to the ``mkdssp``
executable path (e.g. ``setenv DSSP /opt/dssp/mkdssp``)

:issue:`4129`