Dear Gromacs users,
I would like to simulate water diffussion in FER zeolite structure. In the first step, I make a supercell of 336 (xyz) from .cip file. Then I put it in the center of a simulation box (using editconf). As I run the simulation in min, nvt or npt level (in all levels) I face this error:
Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 5832 atoms. The longest distance involved in such interactions is 4.455 nm which is close to half the box length. Either you have excessively large distances between atoms in bonded interactions or your system is exploding.
It should be noted that an initial box size fitting the supercell is defined as I import .pdb file from Avogadro or Material Studio. If I don’t change the predefined box size the simulation goes on without any problem. But, I need to expand the box to add water.
What is the problem? How can I fix it?
Thanks