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 32a358848e5e17f67e76396b2007484d2183874c..882df1162f16e4729c62c5eb75974ff70db3d575 100644 (file)
--- a/docs/release-notes/2022/major/tools.rst
+++ b/docs/release-notes/2022/major/tools.rst
@@ -7,3 +7,49 @@ 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
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The tool now uses the |Gromacs| selection syntax. Rather than piping selections via stdin,
+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.
+
+Some rarely used features have yet to be migrated, including:
+
+- 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
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+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`