Add DSSP v4 support to do_dssp

[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 e35b1f3e8f05bcb4355399eb54dfe051d64d365d..882df1162f16e4729c62c5eb75974ff70db3d575 100644 (file)
--- 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
@@ -30,3 +38,18 @@ Some rarely used features have yet to be migrated, including:
 
 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
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Reporting about file handling and input-file column contents are easier to
+follow.
+
+``gmx do_dssp`` supports DSSP version 4
+"""""""""""""""""""""""""""""""""""""""
+
+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`