Comparison of stability of simulated systems

GROMACS version: 2019.4

GROMACS modification: No

Hi GMX users,

I did 3 MD simulations containing small molecule A + small molecule B + water molecule. The content of simulated systems is as follows:

  1. 2 molecules of A + 2 molecules of B + water molecules
  2. 2 molecules of A + 3 molecules of B + water molecules
  3. 2 molecules of A + 4 molecules of B + water molecules

I need to know which system is more stable energetically relative to others. Which tools or analysis is appropriate for this aim? Is gmx energy good?



Does anyone know the answer to my question in the previous post?

Is gmx energy analysis appropriate?

I want to select one of 3 simulated system based on MD results and then do experimental study on that.


This is a rather difficult question and the answer will not come from energies (enthalpies). You would need to compute free-energies of (effective) interactions between molecules. This is an advanced topic and requires good knowledge of MD simulations and statistical mechanics / thermodynamics.