[gmx-users] Intercalation DNA-Ethidium bromide

[Hovakim Grabski]

Dear Gromacs users,

I've been running several simulations involving 26 base pairs B-DNA  and ethidium bromide.
I used Autodock vina for finding inital binding sites and found one in the small groove.
After that I ran a simulation of 14 ns.
When I check the rmsd of Ethidium Bromide,there's a sudden change.
Is there any chance I could see intercalation?
P.S.  Or I should create an artifical gap between dna bases and then set up a simulation?
Thanks in advance,
Best regards,
Hovakim Grabski