Dear users,
I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to use gmx x2top to get the topology file I see that bonds and angles are not defined correctly. For example, it defines 8 bonds for oxygen atom. This bug was the main problem for segmentation error while running NVT and NPT. What should I do to address this issue? I also attached the pdb file here
Mohammad Rezayani
The issue you're facing with the incorrect bond and angle definitions in the topology file generated by `gmx x2top` is a common problem when dealing with complex crystalline structures like zeolites.
Here are some steps you can try to address this problem:
1. **Check the PDB file quality**: Ensure that the PDB file you generated from the CIF file is accurate and correctly represents the zeolite structure. Verify that the atomic coordinates, connectivity, and symmetry operations are properly captured.
2. **Use a dedicated force field for zeolites**: The standard GROMACS force fields may not be well-suited for accurately describing the complex bonding and connectivity in zeolite structures. Consider using a specialized force field designed for zeolites, such as the Demontis force field or the CLAYFF force field.
3. **Manually define the topology**: Instead of using `gmx x2top`, you can manually create the topology file for your zeolite structure. This will allow you to define the bonds, angles, and other parameters correctly based on the specific force field you're using.
Here's an example of how you can manually define the topology file:
```
[ moleculetype ]
; Name nrexcl
Zeolite 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 Si 1 Zeolite Si1 1 0.0 28.085
2 O 1 Zeolite O1 2 0.0 16.0
3 Si 1 Zeolite Si2 3 0.0 28.085
4 O 1 Zeolite O2 4 0.0 16.0
; Add more atoms as needed
[ bonds ]
; i j func length force.c.
1 2 1 1.60 1000.0
1 3 1 1.60 1000.0
; Add more bonds as needed
[ angles ]
; i j k func angle force.c.
2 1 3 1 109.47 100.0
; Add more angles as needed
```
You can use the `[ atoms ]`, `[ bonds ]`, and `[ angles ]` sections to define the topology for your zeolite structure. Adjust the atom types, bond lengths, and angle values based on the force field you're using.
4. **Consider using alternative tools**: Instead of relying solely on GROMACS, you can explore other molecular simulation software that are better equipped to handle complex crystalline structures like zeolites. For example, you could try using tools like LAMMPS or Hoomd-Blue, which may have better support for zeolite simulations.
By following these steps, you should be able to address the issues with the incorrect bond and angle definitions in the topology file and successfully simulate your zeolite structure in GROMACS.
Good luck; partial credit ai
Dear Mohammad Imam
Thanks a lot for your kind help.
That is completely correct. Actually, my main problem was an initial relaxed structure. When I added water molecules to the zeolite structure in the simulation box, I faced this error. I guess this is because some water molecules were badly positioned within the zeolite and were hindered from being relaxed. I removed the water molecules, and the problem was fixed.
However, I have to make a new setup with separate water molecules and zeolite, letting them relax at the NVT and NPT levels.
I also have another question. In many articles, it is stated that zeolite structures are considered 'rigid.' What does this mean? What changes should I make to the force field parameters? Should I change the interaction parameters to 'zero' or omit them?
Thanks again for your kind help!
Mohammad
Mohammad Rezayani
'rigid' framework of zeolites is relatively inflexible and resistant to deformation compared to other types of materials. This is due to the following characteristics:
1. Covalent bonding: The framework of zeolites is composed of SiO4 and AlO4 tetrahedra connected by strong covalent bonds, which results in a rigid and stable structure.
2. Minimal bond-angle flexibility: The Si-O-Si and Al-O-Si bond angles in zeolites have limited flexibility, which further contributes to the rigidity of the framework.
3. Porous nature: The presence of pores and channels in the zeolite structure also helps to maintain the overall rigidity of the framework.
When modeling zeolite structures using force field parameters, the 'rigidity' of the framework can be accounted for by adjusting the force field parameters as follows:
1. Increase the bond-stretching and angle-bending force constants: To represent the strong covalent bonds and limited bond-angle flexibility, you should increase the values of the bond-stretching and angle-bending force constants in the force field.
2. Decrease the torsional force constants: Since zeolite frameworks have minimal torsional flexibility, you can decrease the torsional force constants in the force field to reflect this.
3. Omit or minimize non-bonded interactions: For some applications, you may choose to omit or minimize the non-bonded interactions (e.g., van der Waals or electrostatic interactions) between atoms within the zeolite framework, as these interactions are typically less significant compared to the strong covalent bonds.
In general, the goal is to capture the essential rigidity of the zeolite framework while still allowing for some flexibility in the structure, particularly when simulating adsorption, diffusion, or other processes that involve guest molecules interacting with the zeolite material.
Good luck; partial credit ai
Dear Mohammad Imam
Thanks again for your comprehensive response!
Mohammad
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