Hold ions in place during md production (system prepared with CHARMM-GUI)

User discussions
1

GROMACS version: 2022.3
GROMACS modification: No

Hi everyone,

I am using CHARMM-GUI for the preparation of a protein which has copper ions inside its structure but I’m having some problems keeping them in their position during the simulation. In gromacs I usually introduce harmonic restraints but I don’t know how to do it within the topology file I obtain from CHARMM-GUI. For avoiding this problem I thought about introducing position restraints with #ifdef…#endif block in the topology and define = -DPOSRES in the mdp file. Is it generally an error using define = -DPOSRES and position restraints also in the md production step?

2

To maintain coordination of an ion, you do not want position restraints, you want distance restraints between ligating atoms and the ion. There are numerous discussions on how to do this in the user forum, search and they should turn up.