Update release notes for gmx msd and clear some TODOs

[alexxy/gromacs.git] / docs / release-notes / 2022 / major / tools.rst

diff --git a/docs/release-notes/2022/major/tools.rst b/docs/release-notes/2022/major/tools.rst
index fdc5086b6992a71ceacef0503ddb83590d5ae4de..5613d2f5bd30acc56ce3be47e6c5b8fc8a4e4cec 100644 (file)
--- a/docs/release-notes/2022/major/tools.rst
+++ b/docs/release-notes/2022/major/tools.rst
@@ -7,20 +7,34 @@ Improvements to |Gromacs| tools
    Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
    a space between the colon and number!
 
-gmx msd has been migrated to the trajectoryanalysis framework
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+``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.
+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.
 
-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`
\ No newline at end of file
+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
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+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.