[gmx-users] Justin-lipid tutorials..

[Justin A. Lemkul]

On 5/19/12 8:23 AM, rama david wrote:
> Thank you Justin ..
> ..
> I goes through these link ..
> http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
>
> Please Can any one clearly define me What is Lower Z and Upper Z in the||
> keepbyz.sh
>
>
> Can keepbyz.sh use to remove the water in hydrophobic region without affecting
> the box dimension ...If yes Then what the value of Lower Z  and Upper Z....
>
>

These values represent the upper and lower bounds of the hydrophobic core of the 
membrane.  They should be set to some reasonable value along the z-axis that 
defines a region in which there should be no water.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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