- Posts: 4
Hybrid model with water
- ODLCS
-
Topic Author
- Offline
- Fresh Boarder
Less
More
6 months 5 days 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
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
Please Log in or Create an account to join the conversation.
- vainikka
-
- Offline
- Admin
Less
More
- Posts: 91
6 months 5 days 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.
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.
Please Log in or Create an account to join the conversation.
- ODLCS
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 4
6 months 3 days 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)
The reason is that the thylakoids parameters are no disponible in Martini 3 (as fas as i know)
Please Log in or Create an account to join the conversation.
Time to create page: 0.090 seconds