- Posts: 21
Freezing simulation in Martini model
- Junb
-
Topic Author
- Offline
- Junior Boarder
Less
More
1 year 2 months ago #9582
by Junb
Freezing simulation in Martini model was created by Junb
Dear Martini developer,
I was wondering if the Martini CG model can be used for freezing simulations/ice nucleation, such as antifreeze protein simulation under ice formation. I know previous Martini water model had some issues, but not sure if this current latest version can do this type of simulation or somehow previous model may work as well?
Thank you so much in advance.
Best,
June
I was wondering if the Martini CG model can be used for freezing simulations/ice nucleation, such as antifreeze protein simulation under ice formation. I know previous Martini water model had some issues, but not sure if this current latest version can do this type of simulation or somehow previous model may work as well?
Thank you so much in advance.
Best,
June
Please Log in or Create an account to join the conversation.
- bart
-
- Offline
- Admin
Less
More
- Posts: 98
1 year 2 months ago #9586
by bart
Replied by bart on topic Freezing simulation in Martini model
The structure of (frozen) water is a very tricky thing and it is not the same as the structure of a LJ fluid (CG water). Actually water can have many structures in its frozen form. If there is a very delicate interaction between the protein and the water (dipoles) I doubt a CG model would be able to give much insight.
However, if the protein for some reasons prefers to be at an interface of a solid and a liquid, things might work out. So I would say it really depends on the mechanism, of which I do not know much.
Short answer: I do not know.
Long answer: could work but probably not. Does PME have any change of improving this, again maybe but probably not. Nevertheless, you do not know if you do not try, unless you have reason to believe there are degrees of freedom missing in the CG model which are required for the phenomena.
However, if the protein for some reasons prefers to be at an interface of a solid and a liquid, things might work out. So I would say it really depends on the mechanism, of which I do not know much.
Short answer: I do not know.
Long answer: could work but probably not. Does PME have any change of improving this, again maybe but probably not. Nevertheless, you do not know if you do not try, unless you have reason to believe there are degrees of freedom missing in the CG model which are required for the phenomena.
Please Log in or Create an account to join the conversation.
- Junb
-
Topic Author
- Offline
- Junior Boarder
Less
More
- Posts: 21
1 year 2 months ago #9590
by Junb
Replied by Junb on topic Freezing simulation in Martini model
Thank you so much for your time and kind reply with such detailed information.
Please Log in or Create an account to join the conversation.
- JessieJim1
-
- Offline
- Fresh Boarder
Less
More
- Posts: 2
11 months 3 weeks ago #9622
by JessieJim1
Replied by JessieJim1 on topic Freezing simulation in Martini model
I would recommend looking into the literature on Martini simulations of ice formation and antifreeze protein simulations to see what approaches have been successful in the past.
Please Log in or Create an account to join the conversation.
Time to create page: 0.163 seconds