# Comparison of stability of simulated systems

**URL:** <https://gromacs.bioexcel.eu/t/comparison-of-stability-of-simulated-systems/3924>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [March 30, 2022, 6:32am UTC](https://gromacs.bioexcel.eu/t/comparison-of-stability-of-simulated-systems/3924 "2022-03-30T06:32:03Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![merry](https://avatars.discourse-cdn.com/v4/letter/m/e480ec/32.png) [@merry](https://gromacs.bioexcel.eu/u/merry)\
**Post date:** [March 30, 2022, 6:32am UTC](https://gromacs.bioexcel.eu/t/comparison-of-stability-of-simulated-systems/3924/1 "2022-03-30T06:32:04Z")

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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

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**Author:** ![merry](https://avatars.discourse-cdn.com/v4/letter/m/e480ec/32.png) [@merry](https://gromacs.bioexcel.eu/u/merry)\
**Post date:** [April 2, 2022, 7:17am UTC](https://gromacs.bioexcel.eu/t/comparison-of-stability-of-simulated-systems/3924/2 "2022-04-02T07:17:31Z")

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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

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [April 5, 2022, 2:22pm UTC](https://gromacs.bioexcel.eu/t/comparison-of-stability-of-simulated-systems/3924/3 "2022-04-05T14:22:20Z")

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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.