Instantaneous positional shifts of protein trajectory

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1

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I performed a 440ns molecular dynamics simulation of a protein homotrimer using GROMACS. After conducting RMSF analysis, I found that the RMSF values of the three monomers fell within different ranges. When I viewed the protein trajectory with VMD, I observed that the entire trimer underwent instantaneous positional shifts in certain frames. Subsequently, I extracted the trajectory file for the first 100ns, and the RMSF values returned to normal. So, I would like to ask what might have caused this movement, whether it led to the abnormal RMSF values, and if there is indeed an issue, how can it be resolved?

2

This sounds like a PBC issue, have you corrected for that in the trajectory?