[gmx-users] Removing Water Molecules

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 6 17:04:00 CET 2012

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?


g_select -select "help all"

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



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


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