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When working with gmx make_ndx I found very annoying the fact that atomic indexes are automatically ranked in the outputted index .ndx file. No matter how the selection is provided, the list of indexes in a group is always ranked.

This is particularly problematic when building indexes for things such dihedral angles, where the ranking is obviously critical.

Is anyone aware of a way to avoid this automatic and un-necessary ranking in the indexes?

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I assume you by "ranking" you mean "sorting numerically" ... I don't think there is a general solution for this in gmx - unless you are ready to do some script writing yourself ...

As a workaround ... in an older gmx version there used to be a tool called mk_angndx

https://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-mk_angndx.html?highlight=mk_angndx

I don't think this is available in more recent versions, so in the worst case you'd need to install the old version locally, use this binary to generate your index file and then use the generated index file with a newer gmx.

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  • $\begingroup$ Good suggestion. It actually looks this feature it's still available: manual.gromacs.org/documentation/2020/onlinehelp/… ... I'll test it! $\endgroup$
    – gluuke
    Commented Jan 7, 2021 at 22:52
  • $\begingroup$ It strictly requires a tpr file as input, while make ndx also accept gro files to build indexes. $\endgroup$
    – gluuke
    Commented Jan 28, 2021 at 9:48

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