MDAnalysis MembraneCurvature

[Nada Taib]

Hi dear users,

I still have some questions about MDAnalysis MembraneCurvature, The major issue is regarding the interpretation of results. If the lipids were randomly distributed, was it expected that the local curvature would be maintained during the all simulation? If the lipid distribution is homogeneous, shouldn't this property fluctuate and average to a constant value in all the bilayer? Also, given the boundary conditions used in MD simulations where the system is replicated in all directions, what is the relevance and meaning of having positive or negative curvature in the center or periphery of the simulated box? How is this related with a higher or lower membrane flexibility?

Thank you very much

Nada

[Estefania Ojeda]

Hi Nada.

I'm sorry for the delay in my reply. Apparently, it never went through. (Attempt #3)

I'll try to answer your questions but please keep in mind that the interpretation of results from MD is system-dependent. We set up very specific simulation systems and perform specific analyses depending on the research question/problem we are addressing.

1) The membrane always fluctuates (due to thermal fluctuations, electrostatic interactions between charge lipid head groups, etc.), regardless of random or homogeneous distributions. The curvature is likely to change, and values of curvature will fluctuate even more if the system is not equilibrated, to the extent that the results obtained may be unrealistic. Hence the importance of reaching an equilibrium state and averaging values.

Ideally, we should run long MD simulations (to reach equilibrium) and run several replicas (to have decent sampling) to obtain a meaningful average (over time and over replicas). But we should be realistic in our research too.

2) If the distribution is homogeneous, your system is equilibrated, and you are calculating an average, that's expected. This is also related to the first Q/A.

3-4) I probably can't answer that. I would assume you are performing a curvature analysis where negative or positive mean/Gaussian curvature has a meaning for you.

Best,

Estefania