On Fri, Jan 6, 2012 at 4:04 PM, Justin A. Lemkul <[email protected]> wrote:
> > > Steven Neumann wrote: > > >> >> On Fri, Jan 6, 2012 at 3:48 PM, Justin A. Lemkul <[email protected]<mailto: >> [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? >> >> > > 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
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
