GROMACS version: 2018.4
GROMACS modification: No
I analyze a few membrane parameters and compare them to the experimental values. I checked area per libid, membrane width, molecular order parameter, C-N angle. Now I want to check water permeation. I found in article “A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers” that they check this water permeation " that they analyzed this parameter. In this article, we can read "MD simulations allow to estimate the water basal permeation across lipid bilayers by counting the water molecules that passed the bilayer in a given time. " but they didn’t write how they do this. They probably write their own scripts, but maybe GROMACS could help me. Is there any tool in GROMACS in which I can measure water permeation? I thought about the script. I would check every 1 ps all water molecules coordination. My lipid bilayer is between z>3.5 and z <7, so if my water molecule will change position from 3.5 to 7 (for example 3.5 in 1 ps, 4.2 in 2ps, 6.1 in 4 ps) I will count them or from 7 to 3.5, but I think it would be hard to do this in the program, so maybe GROMACS could help me or maybe you will have some idea.
It’s not within gromacs, but the LOOS tool crossing-waters can do what you’re looking for.
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