GROMACS version:2023.3
GROMACS modification: Yes/No
Here post your question
I have written the distance restrained information in my topology file for restraining Zn ion with four amino acid it is coordinated with.
The mdrun has successful ran, but the Zn has gone far away.
My .top file is
;
; File ‘p53_wildm.top’ was generated
; By user: kamalesh (1000)
; On host: kamalesh-desktop
; At date: Tue Jul 22 19:08:44 2025
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2021.2 (-:
;
; Executable: /usr/local/gromacs/bin/gmx
; Data prefix: /usr/local/gromacs
; Working dir: /home/kamalesh/Desktop/PHD/test_restrained/distance_res
; Command line:
; gmx pdb2gmx -f p53_wildm.pdb -p p53_wildm.top -o p53_wildm.gro -ignh
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include “amber99sb-ildn.ff/forcefield.itp”
; Include chain topologies
#include “p53_wildm_Protein_chain_A.itp”
#include “p53_wildm_Ion_chain_A2.itp”
; Include water topology
#include “amber99sb-ildn.ff/tip3p.itp”
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include “amber99sb-ildn.ff/ions.itp”
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Ion_chain_A2 1
SOL 210210
NA 2
; restraints for distances
[ intermolecular_interactions ]
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
2642 6037 1 0 1 0.43 0.43 0.43 1000
2685 6037 1 1 1 0.46 0.46 0.46 1000
3606 6037 1 2 1 0.40 0.40 0.40 1000
3653 6037 1 3 1 0.45 0.45 0.45 1000