GROMACS version: GROMACS modification: No Hi @jalemkul I have run the MD simulation (protein-lignad) by following your protocol (http://www.mdtutorials.com/gmx/complex/index.htm). Also at the end of simulation, I recentered and rewrapped the coordinates using gmx trjconv command. In MD simulation movie it gives weird outcome. I ran MD simulation for 200 ns. Energy minimization…