Gmx mdrun outputs a gro file with all atoms having a residue number of 1

User discussions
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 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.

Thank you,
Matthew

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Hi Matthew,

Thanks for the thorough reporting - this sounds odd to me as well. Can help by creating a new issue at

This would be the most direct route to the GROMACS team to address to what seems to be unwanted behaviour!

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Hi Mathew,

Since a few users seem to be having related issues I went ahead and created an issue here

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Thank you very much for taking the time to make an issue. Let’s hope that this problem can get resolved given that other people are experiencing this bug as well.

Best,
Matthew