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Hybrid model with water
- ODLCS
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11 months 1 day ago #9634
by ODLCS
Hybrid model with water was created by ODLCS
HI
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 XXXX microseconds 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
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 XXXX microseconds 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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- xavier
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11 months 1 day ago #9636
by xavier
Replied by xavier on topic Hybrid model with water
Hi,
The modelling of water insertion in proteins while water goes through is a very delicate and complex behaviour that even full atomistic model have issues reproducing.
In the coarse grain model, water is slightly bigger as a basic 4/1 ratio is used. So all the delicate interactions of a water molecule won’t be reproduced … so the penetration of water will be difficult to reproduce.
Such delicate interactions are problematic and the CG model might not be the best. You can try with a full atomistic force field.
I also do believe that smaller waters are available. You can define a proportion of them.
You could give it a trail.
Good luck,
XAvier.
The modelling of water insertion in proteins while water goes through is a very delicate and complex behaviour that even full atomistic model have issues reproducing.
In the coarse grain model, water is slightly bigger as a basic 4/1 ratio is used. So all the delicate interactions of a water molecule won’t be reproduced … so the penetration of water will be difficult to reproduce.
Such delicate interactions are problematic and the CG model might not be the best. You can try with a full atomistic force field.
I also do believe that smaller waters are available. You can define a proportion of them.
You could give it a trail.
Good luck,
XAvier.
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10 months 4 weeks ago #9638
by ODLCS
Replied by ODLCS on topic Hybrid model with water
Thank you so much!
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