Re: [gmx-users] Intercalation DNA-Ethidium bromide

Dear Hovakim Actually it is possible that the ethidium bromide is indeed intercalating in the DNA, because this is expected to happen (experimentally) but if you really see the intercalation, it could be just luck. The time scale needed, in order that such even happens in classical molecular dyna

[gmx-users] Intercalation DNA-Ethidium bromide

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 sudd