GROMACS version:2024.5
GROMACS modification: Yes - PLUMED patched
I created index for amide groups using gmx make_ndx -f run.tpr -o amide_index.ndx and in the prompt entered aN | aHN, my understanding is that I have chosen atoms amide nitrogenN and attached hydrogen HN. However, when I cross checked the indices, they point to Ca and H respectively for all the atoms pairs. I am not able to understand what is wrong? Is this a known issues or I am missing something?