I want to measure water flux across the membrane. This water flux is described here: https://pubs.acs.org/doi/10.1021/acs.jpcb.6b01870 "Water flux across the membrane Based on the number of water molecules that passed the bilayer the water flux F was estimated as F = (NV)/(AT) N is the number of water molecules that passed the bilayer, V the volume of one water molecule, A is the average membrane area, and T the analyzed simulation time (140 ns). "
Do you know how can I do it in GROMACS? I think that I must probably write my own script for that. I think about something like that: checking is there any water in the hydrophobic part of my bilayer and if the water molecule will be on the other side of the bilayer I will count that molecule (so I analyzed where this molecule was before when it is in the hydrophobic part and when it was after). So I must probably check each frame and analyze the z-coordinates of my water molecules. If you have any advice I would be very happy. Thanks in advance.
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