Tool to analyze one leaflet

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
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I have my trajectory .xtc file from a lipid bilayer simulation. Is there a tool that can analyze properties of one leaflet only (such as the area of the inner leaflet)? It seems that gmx energy can only be used to analyze the bilayer but not one leaflet.

Correct me if I’m wrong, but it seems Gridmat MD cannot calculate two separate values for the area per lipid for the two leaflets.

Thanks!

2

gmx energy has no knowledge of what is in the system. The relevant quantities are the box vectors along the plane of the membrane, Box-X and Box-Y. The area is the same for both leaflets, so there’s no need to think of them differently. The APL is then simple:

APL = (Box-X * Box-Y) / (# of lipids in leaflet)

3

Thanks @jalemkul . My lipid bilayer has an additional molecule in one of the leaflets, so I am hoping to treat them separately.

4

Then there is no tool in GROMACS that will give you the quantity you’re after. You may be able to use GitHub - jalemkul/gridmat-md: GridMAT-MD membrane analysis program but it’s geared toward proteins and may require some modifications.

5

@jalemkul I’ll check that out again, thanks!