# Is it possible to measure water flux across the membrane in GROMACS?

**URL:** <https://gromacs.bioexcel.eu/t/is-it-possible-to-measure-water-flux-across-the-membrane-in-gromacs/1586>\
**Category:** User discussions\
**Created:** [February 12, 2021, 5:17pm UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-measure-water-flux-across-the-membrane-in-gromacs/1586 "2021-02-12T17:17:00Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\
**Post date:** [February 12, 2021, 5:17pm UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-measure-water-flux-across-the-membrane-in-gromacs/1586/1 "2021-02-12T17:17:00Z")

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GROMACS version: 2018.4  
GROMACS modification: No

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](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 = (N_V)/(A_T)  
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.