Simulated Annealing of Ethanol water biphasic system

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I wanted to understand the behaviour of small molecules in a biphasic system of ethanol and water. I want to perform simulated annealing with a temperature greater than the boiling point of ethanol but experimentally ethanol evaporates to mimic the experimental conditions and ethanol’s role in simulations how can I handle this problem to construct the system? Looking forward to your help.

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I’m not exactly sure what your question is. Ethanol and water would not be a biphasic system, they mix. So you can just set-up the system to the relevant ethanol/water proportions and then equilibrate it to relevant conditions.

Do you want to run simulated annealing to see ethanol evaporating? In that case, have a look at the Molecular dynamics parameters (.mdp options) - GROMACS 2024.4 documentation section. I’m not sure exactly how well liquid to gas transitions (in a binary mixture) would work, though.

If you want to understand how ethanol evaporation would affect the behaviour of the “small molecules”, you could simply set-up multiple systems with a concentration gradient of ethanol/water.

3

Thank you for your valuable reply. since I don’t want to study the evaporation of ethanol but I want to study the effect of ethanol on small molecule aggregation through simulated annealing. Since during simulated annealing, I am going beyond the boiling point of ethanol which will be physically unrealistic still the ethanol molecule will be present in the system. So, can I run the annealing in two steps: in the presence of ethanol below boiling point to check the ethanol role take the last frame and remove ethanol running beyond its boiling point? It is technically feasible whether the approach is technically correct.

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In principle, it is possible to just remove the ethanol from the last frame (and from the topology (in a separate topology file). However, there are a few issues with that:

  1. Your original system volume must be large enough to maintain a reasonably volume (or box length regarding the cutoff) even after removing the ethanol.
  2. When you remove the ethanol there will be empty volumes in the simulation system. The pressure, temperature and velocities will need to be re-equilibrated.

My suggestion would be to set-up two different systems, one water/ethanol system (with your small molecules) and one pure water system (with your solutes) and run them both. There are still two alternatives:

  1. Run both over the whole range of temperatures, e.g. equilibrate at 290 K and run simulated annealing to 370 K.
  2. Equilibrate the mixture system at 290 K and the water system at 335 K. Run the simulated annealing of the mixture system from 290 K to 360 K. Run the simulated annealing of the water system from 335 K to 370 K.

(The chosen temperature values above are somewhat arbitrary.) In both these cases you get a range of temperatures that overlap between the two systems. You can choose what range of temperatures you use for analysis of the respective system. Also, keep in mind that freezing and boiling temperatures are often not exactly reproduced by most force field parameters.