[gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Jorden Cabal]

Dear Amit,
Your files look correct to me. If "2220" atom in your coordinate file is
the "Zn" atom, it should not be displaced because, from your mdp file and
topology setting  you have restrained all the heavy atoms of Protein, Nad
and Zn. I don't understand why it is happening. Even the restraining force
you are taking is good enough.
I suggest you to check if the atom number 2220 in the co-ordinate file
(.gro file) is Zn atom or not? If it is not then you have wrongly selected
atom number for restraining. Also, if you are following the standard
tutorial for energy minimization which do not restrain any atom, I suggest
you to check the position of Zn atom in structure you get after energy
minimization. If the location of Zn ion is changed during the EM, then you
will need to minimize the system very carefully.
Hope this will fix your issue.
Thank you