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Simulation was done to a DNA-Protein Complex structure with 150mM NACL salt concentration for 100 nanoseconds

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Simulation was done to a DNA-Protein Complex structure with 150mM NACL salt concentration for 100 nanoseconds. The simulation is completed with not much problem, but while visual analysis in VMD of the trajectory, we found the DNA is wavering a lot, even more than protein. Especially 3 nucleotides from one end, which come apart and distort the B-DNA structure. Usually, terminal residues of DNA wavers but in my case, the DNA structure is distorting. What could be the possible reason for such behavior of DNA? Details on tools used; (i) I used AVOGADRO to generate the B-type 12 nucleotide double stranded DNA. The sequence is ATATATATATAT. (ii) I used HADDOCK to dock the protein and DNA, based on some experimental data for the interface.