Dear all Gromacs user, I am using Gromacs to run NVT and NVT equilibrium.
Before the equilibrium, my input gro file shows all atoms (proteins, Zn, Na and Cl ions, and waters) stayed in the box with the periodic condition.
But after equilibrium, the protein itself shows no periodic condition, which means some parts of it are out of box, while otehr atoms remain periodic condition.
I check via VMD and found there are several Zn stay in the box but the protein residues binding with them are out of the box.
How can I fix this? I need Zn stay in Zn-binding domain with the protein whole (not cut by the box).
I am going to run a longer MD. Or this sitiuation won't affect the following MD actually so I don't need to wooried about this?
The screenshot of VMD result was attached.
How to make Zn move along with Zn-binding domain?
To make Zn move together with the Zn-binding domain during a molecular dynamics simulation in GROMACS, you can use a position restraint to keep the Zn ion close to its binding site. Here are the general steps to do this:
1. Set up your system and solvate it using GROMACS tools.
2. Define the Zn-binding domain and the Zn ion as separate groups in the topology file (.top).
3. Create a position restraint file (.itp) for the Zn ion using the following command:
gmx genrestr -f zinc.pdb -o zinc_posre.itp
where zinc.pdb is a file containing the coordinates of the Zn ion.
4. Include the position restraint file in the topology file using the #include statement:
#include "zinc_posre.itp"
5. Add a position restraint force constant to the [ position_restraints ] section of the topology file:
[ position_restraints ]
; atom type fx fy fz
1 2 1000 1000 1000
where atom 1 is the Zn ion and type 2 is the position restraint type specified in the zinc_posre.itp file. The force constant values (fx, fy, fz) will depend on the specific system and should be adjusted to achieve the desired restraint.
6. Run the molecular dynamics simulation as usual, specifying the Zn-binding domain and the Zn ion as separate groups in the .mdp file:
tc-grps = protein SOL NA CL ZN
By applying position restraints, the Zn ion will be kept close to its binding site, allowing it to move together with the Zn-binding domain during the simulation.
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