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Martini box with gas soluted
- dudziu
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2 years 4 months ago #9270
by dudziu
Martini box with gas soluted was created by dudziu
Hello,
I need to create a box, which will contain a Martini model of a protein, water and 2 types of gas (CO2 and O2) solvated.
How do I create such a box?
I need to create a box, which will contain a Martini model of a protein, water and 2 types of gas (CO2 and O2) solvated.
How do I create such a box?
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- xavier
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2 years 4 months ago #9271
by xavier
Replied by xavier on topic Martini box with gas soluted
Hi,
Sounds an interesting idea :)). It shouldn’t be too difficult to put a protein in a box with “vacuum” and/or fill up the space with “gas”.
At this point the real question is how you plan to model the gas? What is their density, isolated and in mixture?
Have you already started to simulate the gas themselves. It sounds like a good start. I am not aware of gas models in Martin-X.
Sounds an interesting idea :)). It shouldn’t be too difficult to put a protein in a box with “vacuum” and/or fill up the space with “gas”.
At this point the real question is how you plan to model the gas? What is their density, isolated and in mixture?
Have you already started to simulate the gas themselves. It sounds like a good start. I am not aware of gas models in Martin-X.
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- dudziu
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2 years 4 months ago #9272
by dudziu
Replied by dudziu on topic Martini box with gas soluted
Yes, modelling a gas molecule is an issue. I know the parameters of a coarse-grain Lennard-Jones 12-6 Force Field of CO2 and O2. They are made of a single bead. Is there a way to create a new bead type in Martini using parameters of a coarse-grain Lennard-Jones 12-6 Force Field?
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2 years 4 months ago #9273
by xavier
Replied by xavier on topic Martini box with gas soluted
Well, it seems you have the solution. Martini has mainly LJ potential between particles, so it should go fine.
You want to look at the definitions of particles and copy an existing one I to your gas. It might get tricky when you mix the gas with other types but if LJ particles, it should go fine.
Gas particles might become popular. I honestly thought that gaz densities were way too deficit to reproduce.
Good luck.
You want to look at the definitions of particles and copy an existing one I to your gas. It might get tricky when you mix the gas with other types but if LJ particles, it should go fine.
Gas particles might become popular. I honestly thought that gaz densities were way too deficit to reproduce.
Good luck.
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