There are inconsistent shifts over periodic boundaries in a molecule type consisting of 31 atoms. Th

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GROMACS version:
GROMACS modification: Yes/No
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i am running gromacs protein-ligand complex tutorial, every step is fine until i reached energy minimization step,

when running gmx mdrun -v -deffnm em i get the error below, i don’t know how to fix it?

There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 31 atoms. The longest distance involved in such interactions is
8.920 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding.

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This error has multiple possible causes so it’s difficult to answer without more details on how the simulation was setup. This post might be helpful