Metal ion moves away from the enzyme during the simulation

[PriZarah]

GROMACS version: 2018.1
GROMACS modification: No
I want to do a md simulation for an enzyme with Pb(II) as a ligand and want to study the interactions formed by meta ion with the amino acid residues of the enzyme. I created the simulation box and placed the metal ion in the active site of the enzyme by replacing a water molecule and started the md simulation. However, after around 20 ns the metal ion started to move away from the enzyme. The simulation was up to 100 ns and at the end of 100 ns, the ion stayed away from the enzyme.
Can anyone please tell me a solution for this?

[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