I tried to make comparison between intra-molecular hydrogen bonds between apo and complex for a protein, but its showing huge difference. i dont know why?
Hai Jürgen Weippert , this image was generated from gromacs. Simulations were performed for apo and complex of same protein. But the intra-molecular hydrogen bonds plot showed much deviation. I dont know the reason for this deviation. I run the simulation for another one protein, the result of that protein is fine.