I have a trajectory containing a solute and many water molecules. Is it possible to compute the energy of the solute through time with GROMACS? I tried gmx energy and make_ndx, but it didn’t work.
You can probably compute the energy terms of the molecule group by using gmx mdrun -rerun and setting the solute as energy group. The function is probably deprecated in new GROMACS version, though. Also, the energy derived with this approach is in general a quantity with a very limited use.