Calculate Ligand self interaction energy

User discussions
1

GROMACS version:2018
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?

2

Hi,

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).

Best regards
Alessandra

3

I want to examine the ligand has interaction with itself or not. If yes calculate it’s energies

4

Hi,
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.

Best regards
Alessandra