Dear All,

I performed MD simulation for DNA-ligand complex for 20 ns using GROMACS v.4.6.5. with AMBER 99SB force field. The ligand topology was obtained using AmberTools 14. The results of RMSD plot of DNA showed that until 6 ns the system seemed relatively stable but after 6 ns onwards there were large fluctuations in RMSD. This to my understanding means that the two strands of DNA are separating off. Are these fluctuations normal or something is wrong with my MD simulation protocol?