Update Groups Can't Be Created for GROMACS2024

User discussions
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1

GROMACS version: 2024
GROMACS modification: No

I’m running simulations for tubulin systems on the AMBER99SB-ILDN forcefield. The simulations run fine, but it seems that -update gpu can’t be passed to mdrun. Upon investigation into the log files for other runs for similar systems that didn’t have -update gpu and were able to run, I find the line “Update groups can not be used for this system because there are three or more consecutively coupled constraints.” I’m unsure what this message means though, or how exactly to fix it.

My protein .itp files come from pdb2gmx, while my ligand .itp files come from AMBER parameter database (Bryce Group: Computational Biophysics and Drug Design - University of Manchester) and are converted to gmx files using parmed. I’ve checked those .itp files, and my hydrogens follow their heavy atoms like the GROMACS user guide says they need to. What else should I be looking for?

2

Hi,
Do you have any molecule where all the hydrogen atoms are listed one after the other for example at the end of a small molecule/ligand? I think this might be one of the reasons that triggers this error.

3

Not as far as I know, I checked both my ligand topologies for that exactly. Would pdb2gmx create anything like that?