# Index groups generated using GMX select do not consist of molecules

**URL:** <https://gromacs.bioexcel.eu/t/index-groups-generated-using-gmx-select-do-not-consist-of-molecules/8580>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [March 12, 2024, 12:22am UTC](https://gromacs.bioexcel.eu/t/index-groups-generated-using-gmx-select-do-not-consist-of-molecules/8580 "2024-03-12T00:22:47Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ok1](https://avatars.discourse-cdn.com/v4/letter/o/9d8465/32.png) [@ok1](https://gromacs.bioexcel.eu/u/ok1)\
**Post date:** [March 12, 2024, 12:22am UTC](https://gromacs.bioexcel.eu/t/index-groups-generated-using-gmx-select-do-not-consist-of-molecules/8580/1 "2024-03-12T00:22:47Z")

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Hello, I have used GMX select-on to select the region and specify the molecule (see figure) . But when I run MSD, there was an error“The index group does not consist of whole molecules,” so I tried to fix it with GMX trjconv-pbc, but GMX TRJCONV can only output a trace file, not an NDX file. So I would like to ask what should be done. Thank you.

 ![f6dfeb61835d9bf64367f45030db54a3](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/304d923640ea398d39943d26a3dba6a905f2e346.png)

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [March 12, 2024, 6:38am UTC](https://gromacs.bioexcel.eu/t/index-groups-generated-using-gmx-select-do-not-consist-of-molecules/8580/2 "2024-03-12T06:38:38Z")

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With that selection string you will only select the atoms that are in the chosen region. I would try to find a selection string that is not as strict regarding the region.

Anyhow, what options do you use to your `gmx msd` command?