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Sucrose monolaurate - MARTINI parameters
- zidarko
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5 years 5 months ago #7824
by zidarko
Sucrose monolaurate - MARTINI parameters was created by zidarko
Hi,
I want to simulate sucrose monolaurate. I have both an all-atom and a coarse grain MARTINI forcefield. For the sucrose part I used the available carbohydrate CG parameters that I modified to include a 4 bead (of type P1) tail.
Now, the issue I have now is that the molecule is supremely hydrophobic. I can for example observe the formation and disruption of aggregates at all-atom but no such thing using the coarse grain.
How do I tone down the hydrophobic character of the laurate chain?
Thanks!
Jernej
I want to simulate sucrose monolaurate. I have both an all-atom and a coarse grain MARTINI forcefield. For the sucrose part I used the available carbohydrate CG parameters that I modified to include a 4 bead (of type P1) tail.
Now, the issue I have now is that the molecule is supremely hydrophobic. I can for example observe the formation and disruption of aggregates at all-atom but no such thing using the coarse grain.
How do I tone down the hydrophobic character of the laurate chain?
Thanks!
Jernej
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- bart
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5 years 5 months ago - 5 years 5 months ago #7825
by bart
Replied by bart on topic Sucrose monolaurate - MARTINI parameters
heya,
I think some things went suboptimal here. For the lauric acid part I would use the parameters you can find in the lipids download section on our webpage. You can find it here . Then the sugar I would use the default sugar model we have for sucrose, which you can find here . Now for the linker things get a bit more interesting.
Using those two as a template it will look like the following if we leave everything as is:
C1-C1-C1-P1(this P1 is the P1 from the sugar)-rest of sugar
To better represent the linker region I would move towards this:
C1-C1-N0-N0(this N0 is the old P1 of the sugar)-rest of sugar
This should give you much better results and actually represent the amphipathic nature of your molecule.
I think some things went suboptimal here. For the lauric acid part I would use the parameters you can find in the lipids download section on our webpage. You can find it here . Then the sugar I would use the default sugar model we have for sucrose, which you can find here . Now for the linker things get a bit more interesting.
Using those two as a template it will look like the following if we leave everything as is:
C1-C1-C1-P1(this P1 is the P1 from the sugar)-rest of sugar
To better represent the linker region I would move towards this:
C1-C1-N0-N0(this N0 is the old P1 of the sugar)-rest of sugar
This should give you much better results and actually represent the amphipathic nature of your molecule.
Last edit: 5 years 5 months ago by bart. Reason: Na to n0
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- zidarko
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5 years 5 months ago - 5 years 5 months ago #7826
by zidarko
Replied by zidarko on topic Sucrose monolaurate - MARTINI parameters
Hi Bart,
This is a great idea. Let me test it out.
It also appears I have used a bead or two too many.
Best,
Jernej
This is a great idea. Let me test it out.
It also appears I have used a bead or two too many.
Best,
Jernej
Last edit: 5 years 5 months ago by zidarko. Reason: Added some more information.
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