GROMACS version:2023.2
GROMACS modification: No
Hello, I am running protein-protein complex with OPLS-AA force field in a cubic box. I got this error at the very first step of Energy minimization. How can I resolve the problem?
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 13037 atoms. The longest distance involved in such interactions
is 9.912 nm which is above half the box length. Either you have excessively
large distances between atoms in bonded interactions or your system is
exploding.
Thank you for your help.
sawsan
since it is happening in the first step of minimization, one possible reason could be that your molecule’s initial coordinates are causing it to break across periodic boundary conditions, or perhaps the box size you’re using doesn’t align well with these coordinates. Additionally, there might be an issue with the generation of your topology file. You might need to consider renumbering the protein sequences.
Thank you for your reply, what do you mean by renumbering the protein sequences?
I really appreciate your help
Best
Saousen