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
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 DEG.gro file which has 17,000 atoms (1000 DEG molecules) in it. The DEG.gro file lists there to be 1000 residues in the left-most column for the 1000 molecules present in the system. Thus, I know the DEG.gro file I use for my input is correct.
However, when I use gmx grompp and gmx mdrun for energy minimization, the resulting out.gro file lists all 17,000 atoms to be listed under residue number 1. I found this problem out when using VMD and finding that the “resid” command did not work properly. For instance, “resid < 2” in VMD will list the entire system instead of just a single molecule, which shows that all of the atoms are listed under a residue number of 1.
Note that this problem did not happen when I used a different computer which had GROMACS installed on it (If I recall correctly, it was a 2018 version). Thus, I think this is a problem related to GROMACS itself rather than any of my files. Nevertheless, I attach the files above just to be thorough. If anyone has a solution to this problem, I would greatly appreciate the help.
UPDATE: I had another colleague run my files and send me their out.gro file from after energy minimization. Note that they used a 2018 version of GROMACS. Their out.gro file DID NOT have this residue number issue.
In addition, on my windows computer at my home, I have Ubuntu installed via the Windows Subsystem for Linux (WSL). Via the WSL, I installed GROMACS and the installation was for the 2020.1 version. However, this problem DID persist when I ran my files on my computer. Since this issue has occurred on two different computers with GROMACS 2020.1 installed, I have come to believe that this is a bug with the 2020.1 version. If someone could look into this, it would be greatly appreciated.