the complex structure (complex.gro )of lysozyme and ultra-small graphene was fine. The steep energy minimization process, nvt and npt process was successfully completed. Additionally, the MD process was observed OK in the beginning. Why the MD process was severely deformed, and the chemical structures of lysozyme and graphene were burst in the end?
There is no issue with your MD-run trajectory. It is just the visualization (This happens due to PBC conditions). Since, you have used gromacs to to the simulation, if you use gromacs itself to do all other analysis then things will be fine and taken care of. But, if you want to save a particular snap or do some analysis of your own, then use "trjconf -f -s -o -ur compact -pbc mol". This will give you a new trajectory which will not have ebroken snaps across boundary.
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