# Mdrun step loses molecular indexes in the output.gro file **URL:** \ **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:** 1\ **Showing post:** 2
**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")
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… --- _[View the full topic](https://gromacs.bioexcel.eu/t/mdrun-step-loses-molecular-indexes-in-the-output-gro-file/209)._