How to solve inconsistent shifts over periodic boundaries in protein-dna run in minimization step?

GROMACS version:2021
GROMACS modification: No
Hi, I want to run a protein-DNA complex with Amber force field in Gromacs. I got this error in the minimization step. what is this problem and how can I solve it?
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 4514 atoms. The longest distance involved in such interactions
is 3.809 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.
I changed my box dimension but the box become so big and my complex did not locate in the center of the PBC box by -c option.
could you help me in this filed?

At which step of the minimization do you get the first error?

Hi
in the first step of minimization. after I run the command “gmx mdrun -v -deffnm em”, the minimization did not start and I got a fatal error “There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 4514 atoms. The longest distance involved in such interactions
is 3.809 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.”. I searched a lot on the internet but I could not find what is the problem and how I can solve it?

A probable explanation is that your in your initial coordinates you molecule is broken over periodic boundary conditions or you use a box size that is incompatible with the coordinates.

I change the box size and type but I got the fatal error again. if my system broke up during simulation how can I fix it? would you mind helping me with this issue? I will send you pictures of my molecule without a box and with the box which fill with water.
thanks so muchpdb

Hi, I faced the same error in the same step. Does anyone know how to fix this issue? Thanks a lot.

Without more detailed information on when this went wrong and what steps you did before that, I cannot say much more.
When changing the box size, you need to be sure that molecules are not broken over pbc.

thanks, Hess
my problem was solved. the problem is not the system broken or the size of the PBC box. it just needed to renumber protein sequences from continuous to non-continues. thanks so much for answering me.
best regards

my problem was solved by just renumbering protein sequence from continuous to non-continous. this erreor was happen due to that topology file make not correctly. just check your pdb file. i wish your problem solved too
best regards