From: Kevin Boyd <kevin44boyd@gmail.com>
Date: Sun, 24 Oct 2021 23:40:40 +0000 (-0700)
Subject: Update release notes for gmx msd and clear some TODOs
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?p=alexxy%2Fgromacs.git;a=commitdiff_plain;h=fc45086679a260d831d4eff3f61738e815897424

Update release notes for gmx msd and clear some TODOs

Fixes #3869
---

diff --git a/docs/release-notes/2022/major/tools.rst b/docs/release-notes/2022/major/tools.rst
index e35b1f3e8f..5613d2f5bd 100644
--- a/docs/release-notes/2022/major/tools.rst
+++ b/docs/release-notes/2022/major/tools.rst
@@ -11,18 +11,26 @@ Improvements to |Gromacs| tools
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 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.
 
+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
diff --git a/src/gromacs/trajectoryanalysis/modules/msd.cpp b/src/gromacs/trajectoryanalysis/modules/msd.cpp
index beae64d65e..0a0dd25616 100644
--- a/src/gromacs/trajectoryanalysis/modules/msd.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/msd.cpp
@@ -391,12 +391,9 @@ struct MsdGroupData
 
 /*! \brief Implements the gmx msd module
  *
- * \todo Implement -(no)mw. Right now, all calculations are mass-weighted with -mol, and not otherwise
  * \todo Implement -tensor for full MSD tensor calculation
  * \todo Implement -rmcomm for total-frame COM removal
  * \todo Implement -pdb for molecule B factors
- * \todo Implement -maxtau option proposed at https://gitlab.com/gromacs/gromacs/-/issues/3870
- * \todo Update help text as options are added and clarifications decided on at https://gitlab.com/gromacs/gromacs/-/issues/3869
  */
 class Msd : public TrajectoryAnalysisModule
 {