GROMACS version:
GROMACS modification: Yes/No
Here post your question : How can I calculate the potential energy of a specific group in GROMACS? I have an index file for the group, but gmx energy doesn’t allow providing an index file directly. Are there alternative methods or tools to achieve this? Any advice would be greatly appreciated!
I am not completely sure but I think you can achieve that by using gmx mdrun -rerun and providing the correct .tpr file that describes your group of interest.