My project is based on MD simulation analysis on a system containing water box and lipid bilayer containing Aquaporin embedded in it. Simulations of timestep 150 ns is performed on this system to study the analysis of water permeation and flow through the lipid bilayer. one of the analysis of my work demands the calculation of water permeation events through each channel of this embedded proteins (this protein contains four monomers forming four water channels). I am performing my analysis using VMD.
I got this script https://www.ks.uiuc.edu/Training/Tutorials/science/nanotubes/files/permeation.tcl surfing from the internet. But this script is not giving the results according to my requirement.
As I wanted to find out permeation events happening through each pore/water channel separately and this script just calculate the water permeation events through the AQP layer as a whole. I have not as much expertise to change this script according to my requirement.