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PIP2(4,5)
- Florian
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9 years 6 months ago #4080
by Florian
PIP2(4,5) was created by Florian
Hello,
I would like to simulate phosphatidylinositol-4,5-bisphosphate (PIP2(4,5)). I have the parameters for PIP2(3,4) from the glycolipids file. Would it make sense to simulate PIP2(4,5) with these parameters or should I change something, for instance the dihedral angle to account for the different position of the phosphate groups?
Florian
I would like to simulate phosphatidylinositol-4,5-bisphosphate (PIP2(4,5)). I have the parameters for PIP2(3,4) from the glycolipids file. Would it make sense to simulate PIP2(4,5) with these parameters or should I change something, for instance the dihedral angle to account for the different position of the phosphate groups?
Florian
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- helgi
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9 years 6 months ago #4083
by helgi
Replied by helgi on topic PIP2(4,5)
Hello, hello,
Indeed in PIP2(3,4) there is a week dihedral that gives some orientational preference to the head group, so PIP2(4,5) would not be the same. In theory you could flip the dihedral to flip the orientation of the headgroup. But I would actually recommend removing the dihedral all to together, this is a weak orientational preference that came from limited testing of atomistic PIPs and will undoubtedly depend on the lipid mixture, PIP concentration etc. etc. so its exact value is most likely not correct in your system anyway (it also makes the PIPs rather computationally unstable so removing it you have a more stable system). Then the PIP2(3,4) and PIP2(4,5) would look the same at the CG Martini level – this of course is not completely correct and it might be possible to model the PIPs more accurately and capture some of their differences even at the CG level, but this will require quite some careful testing and calibrating.
Cheers,
- Helgi
Indeed in PIP2(3,4) there is a week dihedral that gives some orientational preference to the head group, so PIP2(4,5) would not be the same. In theory you could flip the dihedral to flip the orientation of the headgroup. But I would actually recommend removing the dihedral all to together, this is a weak orientational preference that came from limited testing of atomistic PIPs and will undoubtedly depend on the lipid mixture, PIP concentration etc. etc. so its exact value is most likely not correct in your system anyway (it also makes the PIPs rather computationally unstable so removing it you have a more stable system). Then the PIP2(3,4) and PIP2(4,5) would look the same at the CG Martini level – this of course is not completely correct and it might be possible to model the PIPs more accurately and capture some of their differences even at the CG level, but this will require quite some careful testing and calibrating.
Cheers,
- Helgi
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9 years 6 months ago #4084
by Florian
Replied by Florian on topic PIP2(4,5)
Thank you for advice, Helgi!
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