[gmx-users] Removing Water Molecules

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Fri, Jan 6, 2012 at 3:48 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Steven Neumann wrote:
> 
>         Dear Gmx Users,
>          I am setting up the simulation of a protein attached to the
>         half of a nanotube. I set up my system and formed my box and
>         solvated it in TIP3P water. Water molecules obviously were also
>         placed below the part of a nanotube where I do not want them to
>         be. Is there any command which will solvate my system below the
>         surface of the nanotube? Or maybe is there any command or a
>         software that will allow me to remove those unwanted water
>         molecules? I have aroun 26000 water molecules in my system and
>         around 5000 below my nanoutube so with editor it could take
>         ages. Any suggestions?
>          
> 
> 
>     You can use g_select to use geometric criteria, i.e. coordinate
>     value > some number such that only water molecules above a certain
>     point are kept.  Then use trjconv with the index file g_select gives
>     you and you have your cleaned up system.
> 
>     -Justin
> 
> Thank you Justin. That makes sense. Can you please write me which option 
> of g_select will do this? How to see the help for each option?
>  

Try:

g_select -select "help all"

Also note that similar procedures to what you want to do are described in the 
list archive.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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