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

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Fixed bug in gmx order -calcdist
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The reference position for the distance calculation was calculated
wrongly.

Improved grompp usability by rejecting more invalid .mdp lines
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Lines like

    ref-t 298
    = 0.1
    =

are now all rejected with a descriptive message, which will help
prevent some kinds of errors in constructing .mdp inputs. Note that an
.mdp parameter name with a missing value is still accepted, and leads
to the default behavior for that parameter.

Added convert-trj
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A new tool :ref:`convert-trj <gmx convert-trj>` has been added to allow
users to interchange trajectory formats without having to use legacy :ref:`gmx trjconv`.
Supported actions include the generation of slimmed down output trajectories, as well
as the replacement of particle information in individual frames with data from a structure file.
The new tool allows the usage of command line selections, meaning it is no longer
necessary to write :ref:`index <ndx>` files to select certain atoms.
It is part of the drive to split up the :ref:`trjconv <gmx trjconv>` tool
into smaller parts.

Added extract-cluster
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Added a dedicated tool to extract trajectory frames corresponding to different clusters obtained
from :ref:`gmx cluster`. The new :ref:`extract-cluster <gmx extract-cluster>` tool
generates new trajectories that contain only those frames that correspond to the correct cluster.
The corresponding option **-sub** in :ref:`gmx trjconv` has been removed.

Changed behaviour of genion
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Functionality of genion was altered to prevent swapping ions for solvent closer
than -rmin from any other non-solvent atom.
This improvement prevents situations where an ion could be placed at the core
of a protein, which would potentially render the folded protein less stable or
may require long equilibration times.