[gmx-users] Calculating bonded and non-bonded energy for a set of contiguous atoms

[Ashraya Ravikumar]

Hi,

I have the simulation trajectory of a protein. I want to examine the bonded
as well as non-bonded energy for a contiguous set of backbone atoms in the
protein, say starting from C-alpha atom of residue i to C-alpha atom of
residue i+2. I saw that there is an option in the mdp file called
"energygrps" but from what I understood by looking at the documentation and
other discussions, it outputs only non-bonded energy. Is there any way to
get the bonded energy values too?
Thanks in advance.

Regards,
Ashraya Ravikumar