Hi again, I did not quite understand the suggestion. I have successfully added Li+ ions in my simulation box using genion. I am confused about how to place Li+ ions using editconf.
Will I have to create a .gro and .itp file and add it like a solute ? Thanks, Shivangi On Mon, Mar 28, 2011 at 3:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shivangi nangia wrote: > >> Hello, >> >> I am a new gromacs user. >> >> I want to place Li+ ions at a required distance from the polypeptide ( >> which is at the centre of a box of water) >> >> I searched through the archive and the manual if there is a way/provision >> to do this, but could not. >> >> Is there a way? >> > > Measure the distance you want and establish the coordinate at which you > wish to place the ion, then use editconf -center to place it at the proper > location in the simulation box. > > -Justin > > >> >> Please guide. >> >> Thanks, >> Shivangi >> >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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