GROMACS version: 5.1.1
GROMACS modification: No
I pretty new to gromacs and I am confused on how to create an index file? I ran the lysozyme in water tutorial and now I want to conduct further calculations. I am trying to compute the hydrogen bonds between the protein and water, hydrogen bonds within the protein, and hydrogen bonds between water and water. If someone could walk me through how to conduct this that would be great.