1 Improvements to |Gromacs| tools
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5 Please use """"""" to underline the individual entries for fixed issues in the subfolders,
6 otherwise the formatting on the webpage is messed up.
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10 ``gmx msd`` has been migrated to the trajectoryanalysis framework
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13 The tool now uses the |Gromacs| selection syntax. Rather than piping selections via stdin,
14 selections are now made using the "-sel" option. There is a new option called ``-maxtau``,
15 which limits maximum time delta between frames to compare for calculating MSDs. This will allow
16 users who otherwise would run into out-of-memory errors and slow execution with large systems
17 to restrict sampling to useful tau values.
19 This migration comes with about a 20% speedup in execution time.
21 Some rarely used features have yet to be migrated, including:
23 - The -tensor option is not yet implemented.
24 - System COM removal with -rmcomm has not yet been implemented.
25 - B-factor writing using the -pdb option is not yet supported.
27 A slight behavior change is the removal of the -mw option. ``gmx msd`` with ``-mol`` will
28 take the MSD of the center-of-mass of of molecules, while no mass-weighting is done
29 when ``-mol`` is not selected. In previous |Gromacs| versions, ``-mw`` was on by default,
30 and ``-nomw`` was silently ignored when ``-mol`` was chosen. This change will only cause
31 different results when performing MSD calculations on a non-homogenous group of particles without
36 ``gmx chi`` no longer needs ``residuetypes.dat`` entries for custom residues
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39 The need to add the names of custom residues to ``residuetypes.dat`` has been
40 removed, because it served no purpose. This makes ``gmx chi`` easier to use.