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

이종화 jongwha12 at postech.ac.kr
Wed Sep 19 17:47:47 CEST 2012

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,


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