normal Octanol/water

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1 year 11 months ago #9437 by FJSP22
Octanol/water was created by FJSP22
I'm aiming to build a simulation box containing octanol/water in order to estimate partition coefficients of some molecules (I'm using Martini 2.2P and Martini 3.0 force fields). I read the topic below and set x/y compressibility to zero:

cgmartini.nl/index.php/component/kunena/...-and-surface-tension

However, I got some few octanol molecules in the water phase and same behavior of water molecules in octanol phase. I think this kind of configuration it's not good as initial simulation box to estimate partition coefficients of some molecules.
I tried different protocols and I was not able to obtain an two-phase system at final of NpT equilibration. It's very common see this kind of study on literature and I don't know, what are I doing wrong. Should I equilibrate the two solvents separately and only put together during log P calculations (using Umbrella Sampling).
Thanks in advance,

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1 year 11 months ago #9438 by riccardo
Replied by riccardo on topic Octanol/water
Do I understand correctly that you just want to compute the logP of a (small) molecule? If so, then the easiest way to do this is to simulate two pure systems, compute the DG_solvation on the two systems, and do the appropriate arithmetic (i.e., DG_(water-->octanol) = DG_(water-->vacuum) - DG_(octanol-->vacuum)). No need to setup a 2-solvent system. See, among many other references, onlinelibrary.wiley.com/doi/full/10.1002/adts.202100391 , section "2.3. Simulation Settings and Procedure Details" and then the "Free Energies of Transfer Calculations." paragraph. Also note that we usually actually simulate *hydrated* octanol - see again the paragraph I just pointed to.

As for the miscibility, it's indeed expected that octanol and water mix a bit, so the few water molecules in octanol and viceversa makes sense.

I hope this helps.

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1 year 11 months ago #9441 by FJSP22
Replied by FJSP22 on topic Octanol/water
Hi Riccardo!
You always have good suggestions.
Thank you so much for the support.

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