Hi dear users,
I ran a protein-Ligand simulation now I want to calculate ligand self-interaction energies during the simulation, what should I do?
Depends what do you mean self-interaction energies ?
with the option “energygrps” in mdp file you can define groups for which to write short-ranged non-bonded potential energies to the energy file (not supported on GPUs).
I want to examine the ligand has interaction with itself or not. If yes calculate it’s energies
do you mean if the ligand “sees” its periodic images?
Then you can use gmx mindist (with the option -pi) gmx mindist — GROMACS 2021 documentation
if the distance is close the cut-off then the ligand interact with its image and your simulation is biased.