Anomalous coodinates during simumation

[Matteo_Calcagnile]

GROMACS version: 2023
GROMACS modification: No

Hi,
I ran the simulation of a peptide (100 ns). When I view my simulation results using VMD I get an anomalous distribution of the atoms that make up my protein. From the protein start very long bonds that connect atoms several nm away from the rest. What went wrong?

[jalemkul]

Nothing. This is just a periodicity effect. Make molecules whole and remove jumps with trjconv.