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, Steven
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