Mdrun step loses molecular indexes in the output.gro file

GROMACS version: 2020
GROMACS modification: No
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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.


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

Other users seem to have possibly similar issues here:

and here: