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 -- Gromacs Users mailing list
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