[gmx-users] Removing Water Molecules

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Fri, Jan 6, 2012 at 4:04 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Steven Neumann wrote:
> 
> 
> 
>         On Fri, Jan 6, 2012 at 3:48 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto: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
> 
>  
> Thank you. I would appreciate a link of similar problem as I cannot find 
> it at all. Thank you.
>  

Sorry, don't have the time to root through the archive myself.  I know there are 
tons of posts about g_select and examples of use, so I'm sure you'll find them 
if needed.  The help info is probably all you really need.

-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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