Applying distance constraints to ligand and Mg ion

[Tanusha_ghosh]

Hi Josh.

I am also facing a similar situation.
My only confusion is that how you named the Mg and O of ligand as a_10908 and a_10900 respectively?
It seems that you have your gro file to have chain a to be already defined, which I do not have in my case.

FYI, I am attaching the link to my question in the grosmcs mailing forum:

Help with Pulling Simulation Between Two Atoms

GROMACS version: 2025.2 GROMACS modification: No I’m working on a pulling simulation in GROMACS where I want to apply a force between atom N01 of a GUA residue and atom O05 of an ACE group. I’m trying to pull them apart by 1 Å over 0.5 ns, so I’ve set the pull rate to 0.0002 (2 Å/ns). I’m a bit confused about how to correctly define the pull_group1_name and pull_group2_name should I define them based on the residues (GUA and ACE) or create custom index groups for just N01 and O05 ? I’m not s…