[gmx-users] Removing water from sides of bilayer

[Justin A. Lemkul]

krithika krishnaswamy wrote:
> hello,
> 
> Am a new user to gromacs.how to add water to a bilayer.i tried adding 
> water to entire system and then removed water from sides using tcl 
> script.But its not working.
>  
> Is there anyway to build lipid layer by layer and add water or something 
> can be done with genconf,genbox command so that water will not enter 
> middle region of bilayer.Please provide me with a detailed procedure.
> 

There are several options listed on the wiki site:

http://wiki.gromacs.org/index.php/Membrane_Simulations

I find the genbox method to work quite well, myself.  If you're getting water 
from the "sides" of your bilayer, then your box vectors are wrong (i.e., too 
large) for the system.

-Justin

> -krithika
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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