Molecule indexing changed in output after simulation
Users report that output molecule indices are changed unexpectedly to 1 with a change from GROMACS2019 to GROMACS 2020.
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.
Gmx mdrun outputs a gro file with all atoms having a residue number of 1
and possibly related to
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 gromacs 2018 and other while using gromacs 2020. I don’t know whether user forum is a right platform to report this or I need to report this somewhere else. Thank you very much.