[gmx-users] Removing Water Molecules

[Steven Neumann]

On Fri, Jan 6, 2012 at 4:04 PM, Justin A. Lemkul <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>> 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.

Steven
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