[gmx-users] Removing Water Molecules

Steven Neumann s.neumann08 at gmail.com
Fri Jan 6 16:46:24 CET 2012

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?

Thank you,

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