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I was trying to perform lipid bilayer MD for my protein based on GROMACS's Membrane Protein Tutorial.

I can successfully orient the protein in the lipid (turquoise) as you can see in the image below:

enter image description here

But I would like to control the thickness A, B, C of the lipid (before the actual MD run), since I'd like to allow some area of the protein to be exposed outside the lipid (they're extracellular region of the protein).

How can I achieve that with GROMACS?

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You can adjust the thickness of the water layer* by initialising your simulation with more or less water in it.

The thickness of the lipid bilayer is determined by the types of lipids you use, and the force field. Presumably if you build lipids with longer (or shorter) tails you will have a thicker (or thinner) hydrophobic region. You will have to determine for yourself whether the resulting lipid composition is biologically feasible or not.

*If you are simulating in 3D periodic boundary conditions you actually only have one water layer, alternating with the lipid bilayer.

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