Simulations of Interdigitated membrane

User discussions
1

Hello all

I would like to simulate an interdigitated membrane formed with one layer of glycolipids that have two headgroups (bolaform glycolipids, here GSLH). I am using the CHARMM parameters

My question is about the use of the pressure coupling scheme for this type of simulations. Is it 'correct" to use a semiisotropic pressure coupling (instead of for instance the anisotropic pressure coupling) with the following keywords

comm_mode = linear
comm_grps = GSLH SOL

I ask this question because I did not find any papers that simulate similar system.

Any insights (or pointers) of the GROMACS community would be great

Thank you

Stef

2

I would treat your system as any other membrane, interdigitated or not, with respect to COM motion removal and pressure coupling. The use of semiisotropic coupling is standard practice; anisotropic coupling is much less common with membranes.

3

Thank you Justin for your response

I have an additional question : now if my intergitated membrane contains a mixture of two glycolipids (charged and neutral) and that experiments show that the deformation of the membrane increase when the ratio of charged/neutral GL increase. Will the semiisotropic coupling not tend to overstabilize the structure of the membrane ?

Stef

4

I’ve never looked into it, so I have no idea. I don’t know why one would expect semiisotropic coupling to force planarity; the z dimension is free to deform in either anisotropic or semiisotropic coupling schemes.

5

OK thank you Justin