[gmx-users] Removing Water Molecules

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 6 16:48:16 CET 2012

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 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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