# Mdrun step loses molecular indexes in the output.gro file

**URL:** <https://gromacs.bioexcel.eu/t/mdrun-step-loses-molecular-indexes-in-the-output-gro-file/209>\
**Category:** User discussions\
**Created:** [May 28, 2020, 7:18pm UTC](https://gromacs.bioexcel.eu/t/mdrun-step-loses-molecular-indexes-in-the-output-gro-file/209 "2020-05-28T19:18:33Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![cdka229](https://avatars.discourse-cdn.com/v4/letter/c/e47c2d/32.png) [@cdka229](https://gromacs.bioexcel.eu/u/cdka229)\
**Post date:** [May 28, 2020, 7:18pm UTC](https://gromacs.bioexcel.eu/t/mdrun-step-loses-molecular-indexes-in-the-output-gro-file/209/1 "2020-05-28T19:18:33Z")

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GROMACS version: 2020  
GROMACS modification: No  
Here post your question

I switched from 2019 version to the new 2020.2 and having an issue with molecule/fragment indices; I used the same input files from earlier to run the mdrun step using the new version, for an input \*.gro file containing a crystalline supercell of moleules (400 units, each with backbone and side groups fragments separately named and indexed). However, after the mdrun step, all the units have index “1” in front of them. I can however recover the indices back by using the \*.tpr file by using the trjconv function to regenerate \*.gro output.  
Appreciate your advise on this.

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [June 26, 2020, 3:58pm UTC](https://gromacs.bioexcel.eu/t/mdrun-step-loses-molecular-indexes-in-the-output-gro-file/209/2 "2020-06-26T15:58:48Z")

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Hi,

This might be related to an issue we have in GROMACS2020 that is reported here

> **[Molecule indexing changed in output after simulation (#3575) · Issues ·...](https://gitlab.com/gromacs/gromacs/-/issues/3575)**
>
> Users report that output molecule indices are changed unexpectedly to 1 with a change from GROMACS2019 to GROMACS 2020. I switched from 2019 version...

Other users seem to have possibly similar issues here:

> [@Zero protein chain atoms while Indexing a tpr file using gmx 2020 make\_ndx](https://gromacs.bioexcel.eu/t/zero-protein-chain-atoms-while-indexing-a-tpr-file-using-gmx-2020-make-ndx/368):
>
> GROMACS version: Gromacs 2020.2 GROMACS modification: No Hello Everyone, I found a strange thing while working with Gromacs 2020. I have a .tpr file containing the two protein chain A and B. When I was trying to make an index of chain A and chain B using the gromacs 2020 make\_ndx program, it shows 0 atoms. Whereas, when I use the gromacs 2018.1 make\_ndx program for the same task, it works and created an index group of protein chain A and chain B. Please find attached screenshots, one for gr…

and here:

> [@Gmx mdrun outputs a gro file with all atoms having a residue number of 1](https://gromacs.bioexcel.eu/t/gmx-mdrun-outputs-a-gro-file-with-all-atoms-having-a-residue-number-of-1/372):
>
> GROMACS version: 2020.1 GROMACS modification: No Molecule: Diethylene glycol (HOCH2CH2OCH2CH2OH) (17 atoms) Files can be found in google drives: [https://drive.google.com/drive/folders/16HVNNNMcf8ZMSbaqPIyiHM3sISCAcB4w?usp=sharing](https://drive.google.com/drive/folders/16HVNNNMcf8ZMSbaqPIyiHM3sISCAcB4w?usp=sharing) Hello everyone, I am having a problem with the outputted gro file from gmx mdrun. To give you an idea of the problem, I start off with a single\_DEG.gro file which contains a single diethylene glycol molecule (17 atoms). I then use gmx insert-molecules to create a D…