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weria-pezeshkian / FreeDTS

a package to simulate biomembranes at mesoscale
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Can I put the protein on the two side of the membrane? #9

Open BruceLiuIBP opened 3 months ago

BruceLiuIBP commented 3 months ago

Hi, my aim is to place the curvature protein on the two side of the membrane, does it possible to use FreeDTS to do that ?and how can i change the inclusion parameter to do that?

Thank you very much

weria-pezeshkian commented 3 months ago

Hi,

The answer to your question depends on what you want to model. A mesoscale model does not represent molecular details but rather maps their effects. So, if you have one type of protein that binds to a membrane from both sides, this effect can be roughly captured by having two types of inclusions with the same parameters. However, the curvature (c0) of the first one should be the negative of the second one. Additionally, inclusion-inclusion interactions between these two types should be set to zero. This would look something like:

Define 2 Inclusions SRotation Type K KG KP KL C0 C0P C0L 1 Pro1 20 0 0 0 0.4 0 0 1 Pro2 20 0 0 0 -0.4 0 0 Inclusion-Inclusion-Int 1 1 1 0 2 0.0 2 2 1 0 2 0.0 2 2 1 0 0 0.0

BruceLiuIBP commented 2 months ago

Thank you very much for your answer, I think i need to learn more about the membrane biophysics in order to know the parameter definition.