[gmx-users] Justin-lipid tutorials..

Justin A. Lemkul jalemkul at vt.edu
Sat May 19 17:37:16 CEST 2012

On 5/19/12 9:06 AM, rama david wrote:
> Thank you Justin..
> I am sorry Because I am going to ask you the stupid questions but very imp to me ...
> 1.  Consider  your Tutorial In that Instead of using vanderwall radii adjustment
> to add water ,
>      I  wish to use keepbyz.sh script ...
>       In these case What would be the value of Lower and upper Z ..
>       How to find out these hydropbhic region co-ordinate...????

There's nothing really sophisticated to choosing this value.  Look at the 
z-coordinate values of the first hydrophobic carbon in the acyl chains of each 
leaflet.  A ballpark value will suffice to define the boundaries of the 
hydrophobic region.

> 2.  From your reply , I Think Lower and upper  Z is the co-ordinate value , and
> in between these
>      Z-region no water molecule get added...

Basically, but instead it's a post-processing procedure to remove waters, not to 
prevent them from being added (which is done by genbox).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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