+In the process, some old analysis commands have been removed in favor of more
+powerful functionality that is available through an alternative tool.
+For removed or replaced commands, this page documents how to perform the same
+tasks with new tools.
+For new commands, a brief note on the available features is given. See the
+linked help for the new commands for a full description.
+
+This section lists only major changes; minor changes like additional/removed
+options or bug fixes are not typically included.
+
+Version 5.1
+^^^^^^^^^^^
+
+General
+.......
+
+Symbolic links from 5.0 are no longer supported. The only way to invoke a
+command is through :samp:`gmx {<command>}`.
+
+gmx pairdist
+............
+
+**new**
+
+:ref:`gmx pairdist` has been introduced as a selection-enabled replacement for
+:ref:`gmx mindist` (``gmx mindist`` still exists unchanged). It can calculate
+min/max pairwise distances between a pair of selections, including, e.g.,
+per-residue minimum distances or distances from a single point to a set of
+residue-centers-of-mass.
+
+gmx rdf
+.......
+
+**rewritten**
+
+:ref:`gmx rdf` has been rewritten for 5.1 to use selections for specifying the
+points from which the RDFs are calculated. The interface is mostly the same,
+except that there are new command-line options to specify the selections.
+The following additional changes have been made:
+
+* ``-com`` and ``-rdf`` options have been removed. Equivalent functionality is
+ available through selections:
+
+ * ``-com`` can be replaced with a :samp:`com of {<selection>}` as the
+ reference selection.
+ * ``-rdf`` can be replaced with a suitable set of selections (e.g.,
+ :samp:`res_com of {<selection>}`) and/or using ``-seltype``.
+
+* ``-rmax`` option is added to specify a cutoff for the RDFs. If set to a
+ value that is significantly smaller than half the box size, it can speed up
+ the calculation significantly if a grid-based neighborhood search can be
+ used.
+* ``-hq`` and ``-fade`` options have been removed, as they are simply
+ postprocessing steps on the raw numbers that can be easily done after the
+ analysis.
+
+Version 5.0
+^^^^^^^^^^^