Mdrun step loses molecular indexes in the output.gro file

[cblau]

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 ·...

Other users seem to have possibly similar issues here:

Zero protein chain atoms while Indexing a tpr file using gmx 2020 make_ndx

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

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 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…