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

Justin Lemkul jalemkul at vt.edu
Sun Jan 15 18:52:09 CET 2017

On 1/14/17 7:18 AM, Alex Mathew wrote:
> 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
> events,
> http://www.ks.uiuc.edu/Training/Tutorials/science/
> nanotubes/files/permeation.tcl
> 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
> screen.
> Kindly provide your valuable suggestions, since i don't have much expertise
> in coding/programming.

If you define permeation as a water moving into the core of the membrane or 
channel, you can use gmx select to calculate appropriate upper and lower 
boundaries (based on, e.g. upper and lower leaflet P coordinates or some 
suitable amino acids that define the boundaries of the channel) and then 
calculate the number of waters that have an oxygen with a z-coordinate between 
these boundaries.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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