[gmx-users] Ligand-Protein interaction with energy groups

[이종화]

Greetings all,

 

I am trying to compare the stability of two protein-ligand systems where
ligands differ. I am trying to observe the difference of interaction energy
between the ligands. Would it be correct to make energy groups of Protein,
Solvent, Ligand, and compare the energy obtainable by g_energy? I am
confused because in one tutorial I do also have to run simulation with only
the ligand and solvents.

If it were to be correct, would comparing the sum of the LJ-14:Protein-LIG
and Coul-14:Protein-LIG of each ligand be okay?

 

Many thanks in advance,

John