Hi,
I took a look at the snapshots from your previous post and noticed you used a lipid bicelle–like setup for your simulation. However, your bicelle appears to have large hydrophobic defects at the edges, as @obZehn already pointed out, which is a rather energetically unfavorable state.
Have you visualized your trajectory to see how water molecules penetrate the membrane? Also, why choose a bicelle setup to study DNA penetration? A standard bilayer might be easier to handle and carry fewer methodological caveats.
If you do decide to proceed with bicelles, I recommend this paper on bicelle setup (mainly with the MARTINI force field, but adaptable to atomistic simulations).
Best regards,
Marius