[gmx-users] Removing Water Molecules

Steven Neumann s.neumann08 at gmail.com
Fri Jan 6 17:02:35 CET 2012

On Fri, Jan 6, 2012 at 3:48 PM, Justin A. Lemkul <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?

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