Metal ion moves away from the enzyme during the simulation

[alevilla]

Hi,
there are different approaches to describe a metal ions bound to a protein. Of course depending on the question you want to answer one approach may be more suitable of another approach.
One option is to add distance restraint (bond type 6) between the ion and the protein atoms.
Maybe you can have a look at discussions on this topic in the form. see for example

MD simulation for a protein with Cu ions in the structure

GROMACS version:2022.2 GROMACS modification: No Hi everyone, I am currently working with a protein which has 6 Cu ions coordinated in its structure, I would like to know how I need to correctly run the simulation because it’s my first time running a MDS considering ions too. Among the solution I red there is the possibility to use harmonic restraint to restrain the Cu ions to the residues to which they are coordinated using [bonds] type 6 in the topology file. To apply this type of restraint I…

\Alessandra