normal Hybrid model with water

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11 months 3 weeks ago #9635 by ODLCS
Hybrid model with water was created by ODLCS
Hi, everyone:

I have a protein-membrane system solvated with water (all modelled with Martini 2). We are interested in quantifying the water flux through a cavity. Initially, we ran 500 nanoseconds MD simulations and we couldn´t find water models getting into de cavity. About the reasons behind the non-water permeation, we cannot rule out the size of the water models in Martini 2. Is it a reasonable hypothesis. A hybrid model (coarse grained – all atom) would be a good approach to quantify the water flux through cavities?

Oscar

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11 months 3 weeks ago #9637 by vainikka
Replied by vainikka on topic Hybrid model with water
Hi Oscar,

A hybrid model is possible, but very challenging to set up and run correctly.

Is there a particular reason you are using Martini 2? If not, I would suggest using Martini 3, which comes with small and tiny water beads.

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11 months 3 weeks ago #9639 by ODLCS
Replied by ODLCS on topic Hybrid model with water
Hi vainikka,

The reason is that the thylakoids parameters are no disponible in Martini 3 (as fas as i know)

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