Index file

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.


you can create an index file using gmx make_ndx. See this page in the manual for more information.

Kind regards,