[gmx-users] Energy Minimization of DNA

Hello all, how are you doing today? I've been trying to get a stable DNA MD simulation to work for me, but I think my problem lies in an insufficiently energy minimized system prior to running the pr step. I'm using the ffamber99 force field and I've successfully simulated many ns of MD using the

[gmx-users] Example file for DNA

Hello fellow GROMACS users! I've been having a heck of a time with the reformatting of a DNA molecule into a GROMACS-compatible format. I know that residues (bases) must be renamed to DTHR, etc., though it would be endlessly helpful if someone could please send me an example pdb or gmx file I can

[gmx-users] selecting two groups for average structure

Hello, I'm sure there's a simple solution to this problem, so please bear with me... I'm attempting to generate an average structure from a trajectory and I'd like to have it pool two groups into the final structure. I work with a magnesium-coordinating integrase protein, so my groups are 1: prote