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?
Nikhil Maroli
What about other parameters like non bonded interactions and hydrogen bonds?
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Justin Lemkul
Visualize the trajectory. You will see that this is just a consequence of PBC and is easily corrected by using trjconv.
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