Comparison of stability of simulated systems

User discussions
1

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?

Best,
Merry

2

Hi,

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.

Best,
Merry

3

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.