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.
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff