Hi Mohammad,

I think adjusting the box size can solve the error. The box size should be large enough that particles don't interact with both sides of the system, causing PBC errors. Since your MDP file sets short-range cutoffs at 1 nm, ensure that non-solvent particles maintain at least a 1 nm distance from the box edges.

Hope this helps!

Dear Mohammad Assadizadeh

Thank you very much for your reply.

I increased the box size. also, I put a water reservoir on both sides of the zeolite. But, still, I faced a similar error.

However, I think because of the periodicity of the zeolite structure. The zeolite structure is periodic here. As I understood we can not increase box size for peridic structures which seems logical. Actually, I believe I know the problem 99% but I don't know how to fix it. I don't know how we have to behave for such structures with periodicity in Gromacs. Is any special command, or any change in the .mdp files ...???

I don't know!

Hi @Mohammad Re were you able to understand how periodic structures can be simulated in Gromacs? Please let me know.

Dear Somnath Sengupta

in Ifperiodic structures like Zeolite we can not increase the box size and the box size should be exactly equal to the zeolite cell size. In case you want to increase the cell size you should add end groups like O to end Si atoms.

Dear Somnath Sengupta

in the periodic structures like Zeolite we can not increase the box size and the box size should be exactly equal to the zeolite cell size. In case you want to increase the cell size you should add end groups like O to end Si atoms.

To fix the "Non-bonded interaction is larger than table limit" error in GROMACS, ensure that the system is properly solvated and that the cutoff distances are correctly defined. Try the following:

If the problem persists, check for any unusual contacts or configurations that could cause extreme non-bonded interactions.

All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.