[gmx-users] permeation events- ion channels in bilayer

Alex Mathew alexmathewmd at gmail.com
Sat Jan 14 13:18:20 CET 2017

Dear GMX users,

We are looking for water permeation events across the ion-channel, which is
embedded in lipid bilayer. After one micro second MD simulation in
Gromacs2016.1 i used the below script for calculating the  permeation


Unfortunately all the time it gives zero value (I have tried for different
upperEnd  and lowerEnd ), but i can visualize the water movements in VMD

Kindly provide your valuable suggestions, since i don't have much expertise
in coding/programming.


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