On Fri, Jan 6, 2012 at 3:48 PM, Justin A. Lemkul <[email protected]> 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? Steven
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